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Merge levioSAM updates #342

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Merge levioSAM updates #342

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bb5c4c0
levioSAM website additions
BenLangmead Jun 4, 2021
0edb9d7
updating with clearer pointer to sidebar
BenLangmead Jun 4, 2021
e93634f
remove statement about chain files
BenLangmead Jun 5, 2021
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9 changes: 9 additions & 0 deletions doc/website/recent_news.ssi
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<h2>LevioSAM paper and indel-aware major allele references - June 4, 2021</h2>
<ul>
<li>The <a href="https://doi.org/10.1093/bioinformatics/btab396">levioSAM paper</a> is out in the journal <em>Bioinformatics</em>
<li>LevioSAM is a tool that rapidly "lifts" alignments between reference genomes related through a VCF file.
<li>LevioSAM makes it easy to align to one reference with Bowtie 2 (or other aligner), then immediately translate the alignments to a different coordinate system
<li>As a demonstration, we are adding new major-allele versions of human references (GRCh38 and h19) that contain both major-allele SNVs and major-allele (small) indels. Because they include indels, these are more comprehensive than the SNV-only major-allele reference we released previously. LevioSAM provides the ability to translate the alignments back to the original (indel-less) references immediately after. These are in the "Indexes" sidebar on the right.
<li>Detailed instructions on using levioSAM+Bowtie2 in this context are available in the <a href="https://github.com/alshai/levioSAM">levioSAM repo</a> <a href="https://github.com/alshai/levioSAM/blob/master/README.md">README.md</a>
</ul>

<h2>Version 2.4.4 - May 23, 2021</h2>
<ul>
<li>Fixed an issue that would sometimes cause deadlocks in <code>bowtie2</code> when running multithreaded</li>
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46 changes: 44 additions & 2 deletions doc/website/rhsidebar.ssi
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<tr>
<td>
<a href="https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj.zip"><i>H. sapiens</i>, GRCh38 + major SNVs</a>
<a href="https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj_snvs_bt2.zip"><i>H. sapiens</i>, GRCh38 + major SNVs</a>
</td>
<td align="right">
NCBI+1KG
</td>
</tr>
<tr>
<td colspan="2" style="font-size: x-small">&nbsp;&nbsp;<a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/grch38_1kgmaj.fa.gz">FASTA</a>
<td colspan="2" style="font-size: x-small">&nbsp;&nbsp;<a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj_snvs.fa.gz">FASTA</a>
</td>
</tr>

<!-- New as of 6/3/2021 -->
<tr>
<td>
<a href="https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj_snvindels_bt2.zip"><i>H. sapiens</i>, GRCh38 + major SNVs &amp; indels</a>
</td>
<td align="right">
NCBI+1KG
</td>
</tr>
<tr>
<td colspan="2" style="font-size: x-small">&nbsp;&nbsp;<a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="https://github.com/alshai/levioSAM/blob/master/README.md">Use with levioSAM</a>, <a href="https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj_snvindels.fa.gz">FASTA</a>
</td>
</tr>

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</td>
</tr>

<!-- New as of 6/3/2021 -->
<tr>
<td>
<a href="https://genome-idx.s3.amazonaws.com/bt/hg19_1kgmaj_snvs_bt2.zip"><i>H. sapiens</i>, hg19 + major SNVs</a>
</td>
<td align="right">
UCSC+1KG
</td>
</tr>
<tr>
<td colspan="2" style="font-size: x-small">&nbsp;&nbsp;<a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="https://genome-idx.s3.amazonaws.com/bt/hg19_1kgmaj_snvs.fa.gz">FASTA</a>
</td>
</tr>

<!-- New as of 6/3/2021 -->
<tr>
<td>
<a href="https://genome-idx.s3.amazonaws.com/bt/hg19_1kgmaj_snvindels_bt2.zip"><i>H. sapiens</i>, hg19 + major SNVs &amp; indels</a>
</td>
<td align="right">
UCSC+1KG
</td>
</tr>
<tr>
<td colspan="2" style="font-size: x-small">&nbsp;&nbsp;<a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="https://github.com/alshai/levioSAM/blob/master/README.md">Use with levioSAM</a>, <a href="https://genome-idx.s3.amazonaws.com/bt/hg19_1kgmaj_snvindels.fa.gz">FASTA</a>
</td>
</tr>

<tr>
<td>
<a href="https://genome-idx.s3.amazonaws.com/bt/hg18.zip"><i>H. sapiens</i>, hg18</a>
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