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‎_includes/software-content.html‎

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<tr><td colspan="3" style="background-color:#DCEEFF; padding:10px; font-weight:bold; font-size:20px; color:black;">Genome Assembly</td></tr>
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<td class="software-cell" onclick="window.open('https://github.com/birollab/abyss', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/abysslogo.png"><span class="software-title" style="white-space:nowrap;">ABySS <a href="https://github.com/birollab/abyss"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include linuxbrew-icon.html%} brew install abyss</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include bioconda-icon.html%} conda install -c bioconda abyss</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include docker-icon.html%} docker run quay.io/biocontainers/abyss</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Scalable short reads de novo genome assembler</p></td><td class="software-cell" onclick="window.open('https://github.com/birollab/abyss-explorer', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/transparent.png"><span class="software-title" style="white-space:nowrap;">ABySS-explorer <a href="https://github.com/birollab/abyss-explorer"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include linuxbrew-icon.html%} brew install brewsci/bio/abyss-explorer</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Visual exploration of genome sequence assemblies</p></td><td class="software-cell" onclick="window.open('https://github.com/birollab/AIEdit', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/transparent.png"><span class="software-title" style="white-space:nowrap;">AIEdit <a href="https://github.com/birollab/AIEdit"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Machine learning-based genome polisher</p></td></tr>
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<td class="software-cell" onclick="window.open('https://github.com/birollab/abyss', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/abysslogo.png"><span class="software-title" style="white-space:nowrap;">ABySS <a href="https://github.com/birollab/abyss"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include linuxbrew-icon.html%} brew install abyss</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include bioconda-icon.html%} conda install -c bioconda abyss</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include docker-icon.html%} docker run quay.io/biocontainers/abyss</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Scalable short reads de novo genome assembler</p></td><td class="software-cell" onclick="window.open('https://github.com/birollab/abyss-explorer', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/transparent.png"><span class="software-title" style="white-space:nowrap;">ABySSexplorer <a href="https://github.com/birollab/abyss-explorer"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include linuxbrew-icon.html%} brew install brewsci/bio/abyss-explorer</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Visual exploration of genome sequence assemblies</p></td><td class="software-cell" onclick="window.open('https://github.com/birollab/AIEdit', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/transparent.png"><span class="software-title" style="white-space:nowrap;">AIEdit <a href="https://github.com/birollab/AIEdit"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Machine learning-based genome polisher</p></td></tr>
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<td class="software-cell" onclick="window.open('https://github.com/birollab/arcs', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/arcslogo.png"><span class="software-title" style="white-space:nowrap;">ARCS / ARKS <a href="https://github.com/birollab/arcs"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include linuxbrew-icon.html%} brew install brewsci/bio/arcs</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include bioconda-icon.html%} conda install -c bioconda arcs</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include docker-icon.html%} docker run quay.io/biocontainers/arcs</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Genome scaffolder with long or linked reads</p></td><td class="software-cell" onclick="window.open('https://github.com/birollab/GapPredict', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/transparent.png"><span class="software-title" style="white-space:nowrap;">GapPredict <a href="https://github.com/birollab/GapPredict"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">LSTM model for genome gap filling</p></td><td class="software-cell" onclick="window.open('https://github.com/birollab/goldpolish', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/goldpolish-logo.png"><span class="software-title" style="white-space:nowrap;">GoldPolish <a href="https://github.com/birollab/goldpolish"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Genome sequence polisher w/long reads</p></td></tr>
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<td class="software-cell" onclick="window.open('https://github.com/birollab/arcs', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/arcslogo.png"><span class="software-title" style="white-space:nowrap;">ARCS/ARKS <a href="https://github.com/birollab/arcs"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include linuxbrew-icon.html%} brew install brewsci/bio/arcs</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include bioconda-icon.html%} conda install -c bioconda arcs</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include docker-icon.html%} docker run quay.io/biocontainers/arcs</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Genome scaffolder with long or linked reads</p></td><td class="software-cell" onclick="window.open('https://github.com/birollab/GapPredict', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/transparent.png"><span class="software-title" style="white-space:nowrap;">GapPredict <a href="https://github.com/birollab/GapPredict"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">LSTM model for genome gap filling</p></td><td class="software-cell" onclick="window.open('https://github.com/birollab/goldpolish', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/goldpolish-logo.png"><span class="software-title" style="white-space:nowrap;">GoldPolish <a href="https://github.com/birollab/goldpolish"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Genome sequence polisher w/long reads</p></td></tr>
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<td class="software-cell" onclick="window.open('https://github.com/birollab/goldrush', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/goldrushlogo.png"><span class="software-title" style="white-space:nowrap;">GoldRush <a href="https://github.com/birollab/goldrush"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include bioconda-icon.html%} conda install -c bioconda goldrush</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include docker-icon.html%} docker run quay.io/biocontainers/goldrush</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Linear time complexity long read genome assembly</p></td><td class="software-cell" onclick="window.open('https://github.com/birollab/kollector', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/transparent.png"><span class="software-title" style="white-space:nowrap;">Kollector <a href="https://github.com/birollab/kollector"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include linuxbrew-icon.html%} brew install brewsci/science/kollector</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">&nbsp;</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Targeted de novo gene assembly pipeline</p></td><td class="software-cell" onclick="window.open('https://github.com/birollab/abyss', '_blank')" style="vertical-align:top; padding:6px; word-break:break-word; overflow-wrap:anywhere;"><img class="software-logo" src="assets/logos/transparent.png"><span class="software-title" style="white-space:nowrap;">Konnector <a href="https://github.com/birollab/abyss"><img class="git" src="assets/githubicon.svg"></a></span><div style="text-align:center; margin-top:4px;"><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include linuxbrew-icon.html%} brew install abyss</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include bioconda-icon.html%} conda install -c bioconda abyss</div><div style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;">{% include docker-icon.html%} docker run bcgsc/abyss</div></div><p style="padding-top:4px; margin:0; font-weight:bold;">Connecting paired-end reads w/Bloom filter graphs</p></td></tr>
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‎softwareblurbs/abyssexplorer.txt‎

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transparent.png
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ABySS-explorer
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ABySSexplorer
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https://github.com/birollab/abyss-explorer
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brew install brewsci/bio/abyss-explorer
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‎softwareblurbs/arcs.txt‎

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arcslogo.png
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ARCS / ARKS
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ARCS/ARKS
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https://github.com/birollab/arcs
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brew install brewsci/bio/arcs
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conda install -c bioconda arcs

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