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<div class="header-container jumbotron"> | ||
<div class="container"> | ||
<h1>Seqcol: Sequence Collections</h1> | ||
<p>Unique identifiers and lookup service for sequence collections. | ||
</p> | ||
<p><a class="btn btn-primary btn-lg" href="specification" role="button">Learn more</a></p> | ||
</div> | ||
</div> | ||
<div class="container"> | ||
<div class="row"> | ||
<div class="col-md-8"> | ||
<h1 class="header-light regular-pad">What is SeqCol?</h1> | ||
<blockquote> | ||
<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> | ||
</ol> | ||
</p> | ||
<a href="specification">Read the complete specification</a> | ||
</blockquote> | ||
</div> | ||
<div class="col-md-4 text-center"> | ||
<br><br> | ||
<img src="seqcol_abstract_simple.svg" alt="" class="img-responsive"> | ||
</div> | ||
</div> | ||
<hr> | ||
<div class="row"> | ||
<div class="col-sm-4"> | ||
<h1 class="text-center"><i class="fa fa-chart-bar" aria-hidden="true"></i></h1> | ||
<h3 class="text-center">Data analysts</h3> | ||
<p>Uniquely identify the sequences you use with persisent identifiers</p> | ||
</div> | ||
<div class="col-sm-4"> | ||
<h1 class="text-center"><i class="fa fa-wrench" aria-hidden="true"></i></h1> | ||
<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> | ||
</div> | ||
<div class="col-sm-4"> | ||
<h1 class="text-center"><i class="fa fa-cogs" aria-hidden="true"></i></h1> | ||
<h3 class="text-center">Workflow systems</h3> | ||
Use our APIs to retrieve metadata for sequences you use. | ||
</div> | ||
</div> | ||
</div> | ||
# Refget | ||
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Unique identifiers and lookup service for reference sequences and sequence collections. | ||
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<img src="img/seqcol_abstract_simple.svg" alt="Refget abstract" class="img-responsive"> | ||
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## What is refget? | ||
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Refget is a protocol for identifying and distributing biological sequence references. It currently consists of 2 standards: | ||
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1. Refget sequences: a GA4GH-approved standard for individual sequences | ||
2. Refget sequence collections: a standard for collections of sequences, under review | ||
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## What is the refget sequences standard? | ||
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The original refget handled sequences only. Refget enables access to reference sequences using an identifier derived from the sequence itself. | ||
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## What is the refget sequence collections standard? | ||
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*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: | ||
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- 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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