#+TITLE: COVID-19 PubSeq Uploading Data (part 3)
#+AUTHOR: Pjotr Prins
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* Uploading Data

/Work in progress!/

* Table of Contents                                                     :TOC:noexport:
 - [[#uploading-data][Uploading Data]]
 - [[#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]].


* Step 2: Metadata