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Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part3.org')
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diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index 1cd2db1..296bef6 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -13,10 +13,24 @@ * Table of Contents :TOC:noexport: - [[#uploading-data][Uploading Data]] - - [[#table-of-contents][Table of Contents]] - - [[#what-does-this-mean][What does this mean?]] + - [[#introduction][Introduction]] + - [[#step-1-sequence][Step 1: Sequence]] + - [[#step-2-metadata][Step 2: Metadata]] + +* Introduction + +The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a +public resource for global comparisons. Compute it triggered on +upload. Read the [[./about][ABOUT]] page for more information. + +* Step 1: Sequence + +We start with an assembled or mapped sequence in FASTA format. The +PubSeq uploader contains a [[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/qc_fasta.py][QC step]] which checks whether it is a likely +SARS-CoV-2 sequence. While PubSeq deduplicates sequences and never +overwrites metadata it probably pays to check whether your data +already is in the system by querying some metadata as described in +[[./blog?id=using-covid-19-pubseq-part1][Query metadata with SPARQL]]. -* Table of Contents :TOC:noexport: - - [[#what-does-this-mean][What does this mean?]] -* What does this mean? +* Step 2: Metadata |