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# Introduction to SRA Aligned Read Format and Cloud Metadata for SARS-CoV-2
Updated: Jun 2, 2021
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Useful when presenting. --- ### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions - What is the SRA Aligned Read Format - How can I use it? --- ### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives - Understand which data and metadata types are available for SARS-CoV-2 SRA runs in the cloud. - Understand what SRA Aligned Read Format is and what can you do with it. - Working knowledge of SRA Metadata available on the cloud, ways to access it, and some popular use cases. --- # Why have SRA data in the cloud? - SRA data archive format is over 18PB (**great!**) ...but it's a lot of data that is hard to search (**not so great**) - Do you wish: - It was easier to find SRA data based on organismal content? - Searching SRA based on submitted BioProject and BioSample information was simpler? - You could get a sense of what could be assembled out of an SRA dataset before downloading? - You didn't need to do the assembly/variant calling yourself? --- ## What data is in scope for this training? - Public SRA data that contains SARS-CoV-2 sequence - Illumina platform only - Stay tuned for long-read data - How do we determine which runs contain SARS-CoV-2 data? - SRA Taxonomy Analysis Tool (STAT) - Preprint: [doi:10.1101/2021.02.16.431451v1](https://www.biorxiv.org/content/10.1101/2021.02.16.431451v1) --- ## Introduction to SRA aligned read format and associated metadata - Incoming SRA runs are scanned for *Coronaviridae* content - Contigs are created via guided assembly against SARS-CoV-2 RefSeq - fasta contigs - Reads are mapped back to the contigs - aligned sam, fasta/q reads - Taxonomy assessed - STAT - BLAST - Variants are called then annotated with VIGOR3 - VCF --- ## Using aligned read format .pull-left[ - *Coronaviridae* contigs constructed from SRA data - Compatible with SRA Toolkit - Access to reads and contigs individually - Ability to see which reads align to each contig - Smaller size than standard SRA format- no quality scores ] .pull-right[ ![graph with one large node of SRA aligned reads leading to three other nodes: FASTQ, SAM, Fasta contigs (new)](../../images/ncbi/sarf.png) ] --- ## Accessing SRA metadata in the cloud - Cloud query services- BigQuery and Athena - Analyze SRA metadata directly using standard SQL, allowing searches that are not possible in Entrez - No need to manually transform the data for querying, so you can be up and running in just a few minutes - Built in support for complex data fields - You pay for the data scanned, though some free options exist - The underlying metadata files are available for download at no cost - JSON format can be transformed according to your preferences - These can be imported directly to Galaxy --- ## Available SRA metadata SRA aligned read metadata: - User submitted metadata - Biological sample and sequencing library metadata supplied at the time of sequence submission - Contig metadata - Contig stats including: coverage, taxonomy ID, contig length - Taxonomic content analysis of contigs - Search for records based on kmer hits to tax level of interest - BLAST results for contigs - Contig blast results including: hit accession, hit length, percent identity - Variant calls - Variation and VIGOR3 annotation information - Peptides - Details of annotated peptides, including sequence --- ## Popular use cases- what can you do with it? - Finding SARS-CoV-2 contigs with specific coverage and length - Filter SARS-CoV-2 contigs based on geographic location of sample collection - Find top SARS-CoV-2 BLAST hits for contigs from a specific geographic location - Filter for all variations called from samples collected in the United States after 02/01/2021 - Filter for runs with the E484K mutation --- ## SRA data in the cloud .pull-left[ - COVID-focused SRA datasets available in GCP and AWS - Searchable metadata - SRA aligned read files - VCF files - Full SRA runs - Original format submitted files - Benefits - Access large volume of COVID-19-related raw read data with no throttling, at no cost to you - Can be imported into Galaxy for use in your existing workflows ] .pull-right[ .image-100[![screenshot of google cloud ncbi covid-19 project website](../../images/ncbi/covid-cloud.png)] .image-100[![screenshot of aws ncbi covid-19 project website](../../images/ncbi/covid-aws.png)] ] --- ### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points --- ## Thank You! This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!
This material is licensed under the Creative Commons Attribution 4.0 International License