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add in refget docs
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nsheff committed Mar 5, 2024
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74 changes: 27 additions & 47 deletions docs/README.md
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<div class="header-container jumbotron">
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<h1>Seqcol: Sequence Collections</h1>
<p>Unique identifiers and lookup service for sequence collections.
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<p><a class="btn btn-primary btn-lg" href="specification" role="button">Learn more</a></p>
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<h1 class="header-light regular-pad">What is SeqCol?</h1>
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<p><i>Seqcol</i>, or <i>Sequence Collections</i>, is a GA4GH-sponsored <b>community effort to standardize unique identifiers for collections of sequences</b>. Seqcol identifiers can be used to identify genomes, transcriptomes, or proteomes -- anything that can be represented as a collection of sequences. The seqcol protocol provides:
<ol>
<li>implementations of an algorithm for computing sequence identifiers;</li>
<li>a lookup service to retrieve sequences given a seqcol identifier</li>
<li>programmatic approach to assessing compatibility among sequence collections.</li>
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<a href="specification">Read the complete specification</a>
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<img src="seqcol_abstract_simple.svg" alt="" class="img-responsive">
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<h3 class="text-center">Data analysts</h3>
<p>Uniquely identify the sequences you use with persisent identifiers</p>
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<h3 class="text-center">Software developers</h3>
<p>Use Seqcol identifiers to embed persistent information in your tools about what genome was used in an analysis.</p>
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<h3 class="text-center">Workflow systems</h3>
Use our APIs to retrieve metadata for sequences you use.
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# Refget

Unique identifiers and lookup service for reference sequences and sequence collections.

<img src="img/seqcol_abstract_simple.svg" alt="Refget abstract" class="img-responsive">


## What is refget?


Refget is a protocol for identifying and distributing biological sequence references. It currently consists of 2 standards:

1. Refget sequences: a GA4GH-approved standard for individual sequences
2. Refget sequence collections: a standard for collections of sequences, under review

## What is the refget sequences standard?

The original refget handled sequences only. Refget enables access to reference sequences using an identifier derived from the sequence itself.

## What is the refget sequence collections standard?

*Sequence Collections*, or `seqcol` for short, standardizes unique identifiers for collections of sequences. Seqcol identifiers can be used to identify genomes, transcriptomes, or proteomes -- anything that can be represented as a collection of sequences. The seqcol protocol provides:

- implementations of an algorithm for computing sequence identifiers;
- a lookup service to retrieve sequences given a seqcol identifier
- programmatic approach to assessing compatibility among sequence collections.

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