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oschwengers committed Dec 22, 2023
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50 changes: 33 additions & 17 deletions src/views/HomeView.vue
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<template>
<main class="container pt-5">
<div class="row">
<div class="col-md-12 col-lg-6">
<div class="col-md-12 col-lg-10">
<h2>BakRep</h2>
<p>&nbsp;</p>
<p>
The large amount of bacterial genomic data in public genome databases
is an important resource for research in various fields. However, most
of this data has been processed differently, making accurate
comparisons challenging. <em>Blackwell et al</em>., used a uniform
approach to assemble and characterise 661,405 bacterial genomes
retrieved from the European Nucleotide Archive (ENA) in November of
2018. We build up on this resource and further analyse the assembled
genomes in a standardised manner. We conducted a robust taxonomic
classification using the Genome Taxonomy Database (GTDB) and
furthermore subtyped all eligible genomes via multilocus-sequence
typing. In addition we annotated all genomes assigning functional
categories, e.g. COG and E.C., and database cross references to public
databases. The overarching goal is to make this standardised resource
available to non-bioinformaticians via an interactive website. This
website will provide researchers with a flexible search engine to
query the repository
<b>TL;DR</b><br>
>640,000 bacterial genomes, uniformly processed & characterized, enriched with metadata, accessible via a flexible search engine<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- genomic information at your fingertips!
</p>
<p>
Public databases are brimming with bacterial WGS data posing a genetic treasure for many different applications.
However, most analyses focus on particular tiny subgroups that are hard to establish from raw sequencing data or metadata, only.
To this end, BakRep (Denglish blend of Bakterien & Repository) provides access to both comprehensive standardized genome characterizations and metadata via a flexible search engine.
</p>
<p>
BakRep comprises assembly QC metrics, robust taxonomic classifications, MLST typing, genome annotations and original metadata
for a precious collection of bacterial genomes assembled by <a href="https://doi.org/10.1371/journal.pbio.3001421" target="_blank"><em>Blackwell et al</em></a>
</p>
</div>
</div>
<div class="row mt-5">
<div class="col-md-6 col-lg-5">
<div class="card" style="width: 18rem;">
<div class="card-body">
<h5 class="card-title">Search</h5>
<p class="card-text">by characterizations & metadata.</p>
<a href="search" class="btn btn-primary">Search</a>
</div>
</div>
</div>
<div class="col-md-6 col-lg-5">
<div class="card" style="width: 18rem;">
<div class="card-body">
<h5 class="card-title">Browse</h5>
<p class="card-text">by assembly/QC metrics.</p>
<a href="browse" class="btn btn-primary">Browse</a>
</div>
</div>
</div>
</div>
</main>
</template>

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