Jekyll 2026-03-30T10:09:15+00:00 https://training.galaxyproject.org/training-material/topics/sequence-analysis/feed.xml Recently added tutorials, slides, FAQs, and events in the sequence-analysis topic https://training.galaxyproject.org/training-material/assets/images/GTN-60px.png https://training.galaxyproject.org/training-material/topics/sequence-analysis/faqs/quality_score_ES.html 2026-03-30T10:09:15+00:00

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Natalie Kucher https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Helena Vela https://training.galaxyproject.org/training-material/hall-of-fame/hvelab/ Renato Alves https://training.galaxyproject.org/training-material/hall-of-fame/unode/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial_ES.html 2026-03-30T10:09:15+00:00

La secuenciación produce una colección de secuencias sin contexto genómico. No sabemos a

Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ Helena Vela https://training.galaxyproject.org/training-material/hall-of-fame/hvelab/ Renato Alves https://training.galaxyproject.org/training-material/hall-of-fame/unode/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_ES.html 2026-03-30T10:09:15+00:00

Durante la secuenciación, el secuenciador determina las bases nucleotídicas de una muestra de ADN o ARN (biblioteca). Para cada fragmento de la biblioteca se genera una secuencia, también llamada lectura, que no es más que una sucesión de nucleótidos.

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Maria Doyle https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ Alexandre Cormier https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Laura Leroi https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/ Erwan Corre https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/ Stéphanie Robin https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/ Cameron Hyde https://training.galaxyproject.org/training-material/hall-of-fame/neoformit/ Helena Vela https://training.galaxyproject.org/training-material/hall-of-fame/hvelab/ Renato Alves https://training.galaxyproject.org/training-material/hall-of-fame/unode/ Alan O'Cais https://training.galaxyproject.org/training-material/hall-of-fame/ocaisa/ Swathi Nataraj https://training.galaxyproject.org/training-material/hall-of-fame/Swathi266/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/faqs/quality_score_IT.html 2026-03-30T10:08:28+00:00

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Natalie Kucher https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Lisanna Paladin https://training.galaxyproject.org/training-material/hall-of-fame/lisanna/ Silvia Di Giorgio https://training.galaxyproject.org/training-material/hall-of-fame/silviadg87/ Renato Alves https://training.galaxyproject.org/training-material/hall-of-fame/unode/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial_IT.html 2026-03-30T10:08:28+00:00

Il sequenziamento produce una raccolta di sequenze prive di contesto genomico.

Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Lisanna Paladin https://training.galaxyproject.org/training-material/hall-of-fame/lisanna/ Silvia Di Giorgio https://training.galaxyproject.org/training-material/hall-of-fame/silviadg87/ Renato Alves https://training.galaxyproject.org/training-material/hall-of-fame/unode/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_IT.html 2026-03-30T10:08:28+00:00

Durante il sequenziamento, le basi nucleotidiche di un campione di DNA o RNA (detto libreria) vengono determinate dal sequenziatore. Per ogni frammento della libreria viene generata una sequenza, chiamata anche lettura (read), che è semplicemente una successione di nucleotidi.

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Maria Doyle https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ Alexandre Cormier https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Laura Leroi https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/ Erwan Corre https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/ Stéphanie Robin https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/ Cameron Hyde https://training.galaxyproject.org/training-material/hall-of-fame/neoformit/ Swathi Nataraj https://training.galaxyproject.org/training-material/hall-of-fame/Swathi266/ Lisanna Paladin https://training.galaxyproject.org/training-material/hall-of-fame/lisanna/ Silvia Di Giorgio https://training.galaxyproject.org/training-material/hall-of-fame/silviadg87/ Renato Alves https://training.galaxyproject.org/training-material/hall-of-fame/unode/ Alan O'Cais https://training.galaxyproject.org/training-material/hall-of-fame/ocaisa/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/faqs/quality_score_DE.html 2026-03-09T14:19:04+00:00

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Natalie Kucher https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Till Sauerwein https://training.galaxyproject.org/training-material/hall-of-fame/Tillsa/ Renato Alves https://training.galaxyproject.org/training-material/hall-of-fame/unode/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial_DE.html 2026-03-09T14:19:04+00:00

Die Sequenzierung erzeugt eine Sammlung von Sequenzen ohne genomischen Kontext. Wir

Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ Till Sauerwein https://training.galaxyproject.org/training-material/hall-of-fame/Tillsa/ Renato Alves https://training.galaxyproject.org/training-material/hall-of-fame/unode/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_DE.html 2026-03-09T14:19:04+00:00

Bei der Sequenzierung werden die Nukleotidbasen in einer DNA- oder RNA-Probe (Bibliothek) durch den Sequenzierer bestimmt. Für jedes Fragment in der Bibliothek wird eine Sequenz erzeugt, auch Read genannt, die einfach eine Folge von Nukleotiden ist.

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Maria Doyle https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ Alexandre Cormier https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Laura Leroi https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/ Erwan Corre https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/ Stéphanie Robin https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/ Cameron Hyde https://training.galaxyproject.org/training-material/hall-of-fame/neoformit/ Swathi Nataraj https://training.galaxyproject.org/training-material/hall-of-fame/Swathi266/ Till Sauerwein https://training.galaxyproject.org/training-material/hall-of-fame/Tillsa/ Renato Alves https://training.galaxyproject.org/training-material/hall-of-fame/unode/ Alan O'Cais https://training.galaxyproject.org/training-material/hall-of-fame/ocaisa/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/events/2026-03-09-hts-workshop-freiburg.html 2025-10-23T19:56:37+00:00

This course introduces scientists to the data analysis platform Galaxy. The course is designed for beginners; no prior programming skills are required.

Daniela Schneider https://training.galaxyproject.org/training-material/hall-of-fame/Sch-Da/ Diana Chiang Jurado https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Amirhossein Naghsh Nilchi https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ https://training.galaxyproject.org/training-material/events/2025-10-14-foodborne.html 2025-10-13T10:39:07+00:00

The purpose of this workshop is to gain knowledge on detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy. The workshop will be on October 14th 2024 as a 1-day F2F at FHNW Muttenz, Switzerland, free and practical workshop.

Anna Henger https://training.galaxyproject.org/training-material/hall-of-fame/annahenger/ Abdullah Kahraman https://training.galaxyproject.org/training-material/hall-of-fame/abdullahkahraman/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Engy Nasr https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ Santino Faack https://training.galaxyproject.org/training-material/hall-of-fame/santinofaack/ https://training.galaxyproject.org/training-material/events/2025-09-24-wokshop-graz.html 2025-09-23T15:06:50+00:00

This course introduces scientists to the data analysis platform Galaxy. The course is an intermediate course; there is no requirement of any programming skills.

Sebastian Preissl https://training.galaxyproject.org/training-material/hall-of-fame/sebastian-preissl/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Amirhossein Naghsh Nilchi https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/recordings/#tutorial-recording-23-april-2025 2025-04-23T00:00:00+00:00

A 37M long recording is now available.

Deepti Varshney https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ https://training.galaxyproject.org/training-material/events/2025-06-30-hts-workshop-freiburg.html 2025-03-26T13:14:41+00:00

This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required.

Daniela Schneider https://training.galaxyproject.org/training-material/hall-of-fame/Sch-Da/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Diana Chiang Jurado https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/ Engy Nasr https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ Mina Hojat Ansari https://training.galaxyproject.org/training-material/hall-of-fame/Minamehr/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/workflows/main_workflow.html 2025-03-26T11:29:27+00:00

Deepti Varshney https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html 2025-03-26T11:29:27+00:00

The regulated expression of genes is essential for defining morphology, functional capacity, and developmental fate of both solitary living cells as well as cells inhabiting the social environment of a multicellular organism. In this regard, the regulation of transcription, that is, the synthesis of messenger RNA from a genomic DNA template, plays a crucial role. It contributes to the control of temporal and spatial RNA and protein levels in a cell and therefore has an essential function in all living organisms. Transcription‐associated proteins (TAPs) are essential players in gene regulatory networks (GRNs) as they involved in transcriptional regulation. TAPs are broadly classified into transcription factors (TFs) and transcriptional regulators (TRs). TFs bind sequence‐specifically to regulatory elements, resulting in enhancing or repressing of transcription (Richardt et al. 2007; Wilhelmsson et al. 2017). TRs, on the other hand, are involved in protein–protein interactions, may serve as regulators at the transcriptional core complex, as co‐activators and co‐repressors, chromatin modification or methylation. Additionally, there are proteins referred to as putative TAPs (PTs) that are thought to be involved in the regulation of transcription, but their exact function is undefined (Richardt et al. 2007).

Deepti Varshney https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/viral_primer_design/workflows/main_workflow.html 2025-03-20T08:06:12+00:00

Primer design of related virus gene sequences.

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html 2025-03-20T08:06:12+00:00

Modern molecular, DNA and RNA-based methods have seen ever increasing use, over the last decades, in the detection and analysis of viral pathogens. Most of these methods rely on PCR for amplification of viral DNA/RNA and are, thus, dependent on primers that recognize viral targets reliably and selectively. Designing such primers can be challenging if the diversity of viral genotypes that need to be recognized by the primers is high.

Verena Moosmann https://training.galaxyproject.org/training-material/hall-of-fame/VerenaMoo/ Elischa Berger https://training.galaxyproject.org/training-material/hall-of-fame/elischberg/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Verena Moosmann https://training.galaxyproject.org/training-material/hall-of-fame/VerenaMoo/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/recordings/#tutorial-recording-18-march-2025 2025-03-18T00:00:00+00:00

A 37M long recording is now available.

Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ https://training.galaxyproject.org/training-material/events/2025-03-10-hts-workshop-freiburg.html 2024-10-15T12:38:08+00:00

This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required.

Daniela Schneider https://training.galaxyproject.org/training-material/hall-of-fame/Sch-Da/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Amirhossein Naghsh Nilchi https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Engy Nasr https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_IT.md#tutorial-recording-30-september-2024 2024-09-30T00:00:00+00:00

A 51M long recording is now available.

Diana Chiang Jurado https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_ES.md#tutorial-recording-30-september-2024 2024-09-30T00:00:00+00:00

A 51M long recording is now available.

Diana Chiang Jurado https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_DE.md#tutorial-recording-30-september-2024 2024-09-30T00:00:00+00:00

A 51M long recording is now available.

Diana Chiang Jurado https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/recordings/#tutorial-recording-30-september-2024 2024-09-30T00:00:00+00:00

A 51M long recording is now available.

Diana Chiang Jurado https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial_IT.md#tutorial-recording-7-september-2024 2024-09-07T00:00:00+00:00

A 24M long recording is now available.

Dinithi Rajapaksha https://training.galaxyproject.org/training-material/hall-of-fame/DinithiRajapaksha/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial_ES.md#tutorial-recording-7-september-2024 2024-09-07T00:00:00+00:00

A 24M long recording is now available.

Dinithi Rajapaksha https://training.galaxyproject.org/training-material/hall-of-fame/DinithiRajapaksha/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial_DE.md#tutorial-recording-7-september-2024 2024-09-07T00:00:00+00:00

A 24M long recording is now available.

Dinithi Rajapaksha https://training.galaxyproject.org/training-material/hall-of-fame/DinithiRajapaksha/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/recordings/#tutorial-recording-7-september-2024 2024-09-07T00:00:00+00:00

A 24M long recording is now available.

Dinithi Rajapaksha https://training.galaxyproject.org/training-material/hall-of-fame/DinithiRajapaksha/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-contamination-control/recordings/#tutorial-recording-1-august-2024 2024-08-01T00:00:00+00:00

A 34M long recording is now available.

Clea Siguret https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-contamination-control/workflows/Quality-and-contamination-control-in-bacterial-isolate-using-Illumina-MiSeq-Data.html 2024-07-15T10:02:19+00:00

Quality and contamination control in bacterial isolate using Illumina MiSeq Data

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Clea Siguret https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html 2024-07-15T10:02:19+00:00

Sequencing (determining of DNA/RNA nucleotide sequence) is used all over the world for all kinds of analysis. The product of these sequencers are reads, which are sequences of detected nucleotides. Depending on the technique these have specific lengths (30-500bp) or using Oxford Nanopore Technologies sequencing have much longer variable lengths.

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Clea Siguret https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/ Verena Moosmann https://training.galaxyproject.org/training-material/hall-of-fame/VerenaMoo/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Clea Siguret https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ https://training.galaxyproject.org/training-material/events/2024-07-22-freiburg-july.html 2024-07-10T17:01:39+00:00

This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required.

Anika Erxleben https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Amirhossein Naghsh Nilchi https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Engy Nasr https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ https://training.galaxyproject.org/training-material/events/2024-09-10-biont-rnaseq.html 2024-07-03T08:50:25+00:00

Join us for an engaging 4-half day online workshop and dive into the captivating world of RNA-seq data analysis using Galaxy! This hands-on workshop will equip you with the skills to effectively analyze RNA-seq data from start to finish. You will learn about: Galaxy, Quality Control, Mapping and Quantification and Downstream Analysis. Don't miss this opportunity to enhance your bioinformatics skills.

Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/ncbi-fcs/workflows/NCBI-Foreign-Contamination-Screen.html 2024-04-16T09:25:46+00:00

This workflow performs contamination cleaning steps on assembled genomes. Users specify an input genome (fasta/fasta.gz) and taxonomic information corresponding to the source organism. There are two screening steps for foreign organism sequences (FCS-GX) and adaptors (FCS-adaptor), each followed by a cleaning step to remove identified contaminants. The final output is a cleaned genome.

National Center for Biotechnology Information https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.html 2024-04-16T09:25:46+00:00

The National Center for Biotechnology Information (NCBI) performs contamination screening of genome assemblies submitted to the archival GenBank. Advances in genome sequencing have accelerated the production of genome assemblies and their submission to public databases, necessitating high-performance screening tools. Since contaminants can lead to misleading conclusions about the biology of the organism in question (e.g. gene content, gene evolution, etc.), ideally contamination screening should be performed after the initial contig assembly and prior to downstream genome analyses.

Eric Tvedte https://training.galaxyproject.org/training-material/hall-of-fame/tvedtees/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Eric Tvedte https://training.galaxyproject.org/training-material/hall-of-fame/tvedtees/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.html 2024-01-08T11:21:03+00:00

Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1_From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.html 2024-01-08T11:21:03+00:00

Coline Royaux https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html 2024-01-08T11:21:03+00:00

The objective of this tutorial is to learn how to clean and manage AB1 data files freshly obtained from Sanger sequencing.

Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/faqs/quality_score.html 2023-07-10T11:58:19+00:00

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Natalie Kucher https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.html 2023-07-10T11:58:19+00:00

There is a growing need for undergraduate students to learn cutting-edge concepts in genomics data science, including performing analysis on the cloud instead of a personal computer.

Natalie Kucher https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/ Ava Hoffman https://training.galaxyproject.org/training-material/hall-of-fame/avahoffman/ Robert Meller https://training.galaxyproject.org/training-material/hall-of-fame/robertmeller/ Katherine Cox https://training.galaxyproject.org/training-material/hall-of-fame/katherinecox/ Frederick Tan https://training.galaxyproject.org/training-material/hall-of-fame/cutsort/ Natalie Kucher https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/ Candace Savonen https://training.galaxyproject.org/training-material/hall-of-fame/cansavvy/ Ava Hoffman https://training.galaxyproject.org/training-material/hall-of-fame/avahoffman/ Elizabeth Humphries https://training.galaxyproject.org/training-material/hall-of-fame/ehumph/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_IT.md#tutorial-recording-19-may-2023 2023-05-19T00:00:00+00:00

A 50M long recording is now available.

Andrew Lonsdale https://training.galaxyproject.org/training-material/hall-of-fame/LonsBio/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_ES.md#tutorial-recording-19-may-2023 2023-05-19T00:00:00+00:00

A 50M long recording is now available.

Andrew Lonsdale https://training.galaxyproject.org/training-material/hall-of-fame/LonsBio/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_DE.md#tutorial-recording-19-may-2023 2023-05-19T00:00:00+00:00

A 50M long recording is now available.

Andrew Lonsdale https://training.galaxyproject.org/training-material/hall-of-fame/LonsBio/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/recordings/#tutorial-recording-19-may-2023 2023-05-19T00:00:00+00:00

A 50M long recording is now available.

Andrew Lonsdale https://training.galaxyproject.org/training-material/hall-of-fame/LonsBio/ https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html 2023-04-13T15:51:25+00:00

This learning path aims to teach you the basics of Galaxy and analysis of sequencing data. You will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences.

https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html 2023-01-16T08:13:56+00:00

MAdLandDB is a protein database comprising of a comprehensive collection of fully sequenced plant and algal genomes, with a particular emphasis on non-seed plants and streptophyte algae. Additionally, for comparative analysis, the database also includes genomes from various other organisms such as fungi, animals, the SAR group, bacteria, and archaea. The database is actively developed and maintained by the Rensing lab and released in the MAdLand setting. It employs a system of species abbreviation using a 5 letter code, which is constructed using the first three letters of the genus and the first two letters of the species name, for example, CHABR for Chara braunii. Furthermore, the database provides gene identification through the addition of gene ID’s and supplementary information such as the encoding source of the gene, whether it is plastome encoded (pt) or transcriptome-based (tr) in cases when a genome is not yet available. The key advantage of this database is its non-redundant nature, and the fact that all sequences are predominantly from genome projects, thereby increasing their reliability.

Deepti Varshney https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Deepti Varshney https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/faqs/fastq.html 2022-09-29T12:40:13+00:00

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/faqs/snp.html 2022-03-02T15:46:20+00:00

SNP (pronounced “snip”) stands for Single Nucleotide Polymorphism. This means a single nucleotide change as compared to the reference genome.

Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/faqs/perbase_warning.html 2022-03-02T15:46:20+00:00

So far it does not mean that your data is bad. Your protocol or your data might have a bias that you normally expect. Check first the following things:

Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/faqs/multiqc_error.html 2022-03-02T15:46:20+00:00

Please double-check that:

Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/faqs/jbrowse_runtime.html 2022-03-02T15:46:20+00:00

Normally this should be done in around 3 minutes. However, it might be busy on the servers, so please be patient and come back to it later.

Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/faqs/further_learning.html 2022-03-02T15:46:20+00:00

I really like QCFAIL, It has some nice user stories of quality control issues encountered in real data and experiments

Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.html 2021-08-04T12:11:40+00:00

Removal of human reads from SARS-CoV-2 sequencing data

https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html 2021-08-04T12:11:40+00:00

Patient samples for pathogen detection are usually “contaminated” with human host DNA.

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/recordings/#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 10M long recording is now available.

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial_IT.md#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 20M long recording is now available.

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial_ES.md#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 20M long recording is now available.

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial_DE.md#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 20M long recording is now available.

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/recordings/#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 20M long recording is now available.

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/recordings/#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 40M long recording is now available.

Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_IT.md#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 1H10M long recording is now available.

Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_ES.md#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 1H10M long recording is now available.

Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial_DE.md#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 1H10M long recording is now available.

Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/recordings/#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 1H10M long recording is now available.

Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping.html 2018-09-20T07:18:11+00:00

Mapping

Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/workflows/quality_control.html 2017-06-27T15:55:22+00:00

Quality Control

https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/slides.html 2016-10-04T14:08:30+00:00

Example NGS pipeline

Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Engy Nasr https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Anup Kumar https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html 2016-10-04T14:08:30+00:00

Sequencing produces a collection of sequences without genomic context. We do not know to which part of the genome the sequences correspond to. Mapping the reads of an experiment to a reference genome is a key step in modern genomic data analysis. With the mapping the reads are assigned to a specific location in the genome and insights like the expression level of genes can be gained.

Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Mehmet Tekman https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/ Ekaterina Polkh https://training.galaxyproject.org/training-material/hall-of-fame/polkhe/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ Maria Doyle https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/slides.html 2016-10-04T13:22:53+00:00

Why Quality Control?

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Alexandre Cormier https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/ Laura Leroi https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/ Erwan Corre https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/ Stéphanie Robin https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/ Swathi Nataraj https://training.galaxyproject.org/training-material/hall-of-fame/Swathi266/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Mateo Boudet https://training.galaxyproject.org/training-material/hall-of-fame/mboudet/ Alexandre Cormier https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html 2016-10-04T13:22:53+00:00

During sequencing, the nucleotide bases in a DNA or RNA sample (library) are determined by the sequencer. For each fragment in the library, a sequence is generated, also called a read, which is simply a succession of nucleotides.

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Maria Doyle https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ Alexandre Cormier https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Laura Leroi https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/ Erwan Corre https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/ Stéphanie Robin https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/ Cameron Hyde https://training.galaxyproject.org/training-material/hall-of-fame/neoformit/ Swathi Nataraj https://training.galaxyproject.org/training-material/hall-of-fame/Swathi266/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Anne Fouilloux https://training.galaxyproject.org/training-material/hall-of-fame/annefou/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Natalie Kucher https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Matthias Bernt https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/ Anup Kumar https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/ Anika Erxleben https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/ Maria Doyle https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Simon Bray https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/ Mateo Boudet https://training.galaxyproject.org/training-material/hall-of-fame/mboudet/ Alexandre Cormier https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/