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index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>GitHub Pages Index</title>
</head>
<body>
<h1>Welcome the JHU/APL Biological Sciences Datasets Directory</h1>
<h2>Reference Links</h2>
<ul>
<li><a href="https://github.com/jhuapl-bio/taxtriage/">TaxTriage</a></li>
<li><a href="https://github.com/jhuapl-bio/basestack/">Basestack</a></li>
<li><a href="https://benlangmead.github.io/aws-indexes/k2">Kraken2 databases to download or use</a></li>
<li><a href="https://github.com/jhuapl-bio/GE-Workshop-Sandbox/blob/main/Advanced_Metagenomics.md">Pre install session - metagenomics </a></li>
<li><a href="https://github.com/DerrickWood/kraken2">Kraken2</a></li>
<li><a href="https://www.nextflow.io/docs/latest/index.html">Nextflow</a></li>
<li><a href="https://nf-co.re/">nf-core</a></li>
<li><a href="https://www.docker.com/">Docker</a></li>
<li><a href="https://jhuapl-bio.github.io/mytax/">Mytax2</a></li>
<li><a href="https://fbreitwieser.shinyapps.io/pavian/">Pavian</a></li>
</ul>
<h2>Download Install Files</h2>
<ul>
<li><a download="install.bat" href="install.bat">Installation BAT file</a></li>
<li><a download href="wsl.bat">Install WSL dependencies file</a></li>
<li><a download href="install_bundle.sh">Install For Linux/Mac Script File</a></li>
<li><a download href="install.sh">Full commands unix install</a></li>
</ul>
<h2>Download kraken2 databases</h2>
<ul>
<li><a href="https://github.com/jhuapl-bio/datasets/raw/main/databases/kraken2/test_metagenome.tar.gz">Test</a></li>
<li><a href="https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20230605.tar.gz">Standard Refseq 8 GB</a></li>
<li><a href="https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20230605.tar.gz">Viral (Refseq)</a></li>
<li><a href="https://media.githubusercontent.com/media/jhuapl-bio/mytax/master/databases/flukraken2.tar.gz">Flukraken2</a></li>
<li><a href="https://benlangmead.github.io/aws-indexes/k2">All Others</a></li>
</ul>
<h2>Fastq Reads</h2>
<ul>
<li><a href="fastq/miseq_reads_R1.fasta.gz">Short Reads R1</a></li>
<li><a href="fastq/miseq_reads_R1.fasta.gz">Short Reads R2</a></li>
<li><a href="fastq/ont_reads.fastq.gz">Long Reads Fastq</a></li>
</ul>
<h2>Download a Reference FASTA</h2>
<ul>
<li><a href="references/test.fasta">Test Metagenomics References</a></li>
<li><a href="references/test.fasta.fai">Test References Index</a></li>
</ul>
<h2>Alignment File</h2>
<ul>
<li><a href="alignment/miseq.bam">Illumina Short Reads Alignment File (BAM)</a></li>
<li><a href="alignment/miseq.bam.bai">Indexed BAM file for the above</a></li>
</ul>
<h2>Alignment Histogram of Coverage</h2>
<ul>
<li><a href="alignment/miseq.histogram">Illumina Short Reads Cov. Histogram</a></li>
</ul>
<h2>Kraken2 Outputs</h2>
<ul>
<li><a href="kraken2/miseq.k2.report">Miseq Kraken2 output</a></li>
<li><a href="kraken2/ont.k2.report">ONT Kraken2 output</a></li>
</ul>
<h2>Krona Outputs</h2>
<ul>
<li><a href="krona/ont.krona.html">ONT Omics Workshop Krona Example</a></li>
<li><a href="krona/miseq.krona.html">Miseq Omics Workshop Krona Example</a></li>
<li><a href="krona/nanosim_metagenome.fastq.html">Long Reads Krona Output</a></li>
<li><a href="krona/shortreads.krona.html">Short Reads Krona Output</a></li>
<li><a href="krona/nanosim_metagenome.fastq.viral.html">Long Reads Viral - Bad DB</a></li>
<li><a href="krona/iss_reads_R1.fastq.viral.html">Short Reads Krona Viral - Bad DB</a></li>
</ul>
<footer>
<p>Generated for GitHub Pages</p>
</footer>
</body>
</html>