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| <title>ea-utils by ExpressionAnalysis</title> | |
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| <h1>ea-utils</h1> | |
| <h2>FASTQ processing utilities</h2> | |
| <a href="https://github.com/ExpressionAnalysis/ea-utils" class="button"><small>View project on</small> GitHub</a> | |
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| <h1> | |
| <a id="ea-utils-has-migrated-to-github-from-httpscodegooglecompea-utils" class="anchor" href="#ea-utils-has-migrated-to-github-from-httpscodegooglecompea-utils" aria-hidden="true"><span class="octicon octicon-link"></span></a>ea-utils has migrated to GitHub from <a href="https://code.google.com/p/ea-utils/">https://code.google.com/p/ea-utils/</a> | |
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| <a id="overview" class="anchor" href="#overview" aria-hidden="true"><span class="octicon octicon-link"></span></a>Overview:</h1> | |
| <p>Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. | |
| Primarily written to support an Illumina based pipeline - but should work with any FASTQs.</p> | |
| <ul> | |
| <li> | |
| <strong><a href="https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMcf.md">fastq-mcf</a></strong> - Scans a sequence file for adapters, and, based on a log-scaled threshold, determines a set of clipping parameters and performs clipping. Also does skewing detection and quality filtering.</li> | |
| <li> | |
| <strong><a href="https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMultx.md">fastq-multx</a></strong> - Demultiplexes a fastq. Capable of auto-determining barcode id's based on a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify that the reads are in-sync as well, and fail if they're not.</li> | |
| <li> | |
| <strong><a href="https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqJoin.md">fastq-join</a></strong> - Similar to audy's stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It uses the same "squared distance for anchored alignment" as other tools.</li> | |
| <li> | |
| <strong><a href="https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/Varcall.md">varcall</a></strong> - Takes a pileup and calculates variants in a more easily parameterized manner than some other tools.</li> | |
| </ul> | |
| <h1> | |
| <a id="other-stuff" class="anchor" href="#other-stuff" aria-hidden="true"><span class="octicon octicon-link"></span></a>Other Stuff:</h1> | |
| <ul> | |
| <li> | |
| <strong><a href="https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/SamStats.md">sam-stats</a></strong> - Basic sam/bam stats. Like other tools, but produces what I want to look at, in a format suitable for passing to other programs. </li> | |
| <li> | |
| <strong>fastq-stats</strong> - Basic fastq stats. Counts duplicates. Option for per-cycle stats, or not (irrelevant for many sequencers). </li> | |
| <li> | |
| <strong>determine-phred</strong> - Returns the phred scale of the input file. Works with sams, fastq's or pileups and gzipped files.</li> | |
| <li> | |
| <strong>Chrdex.pm</strong> & <strong>Sqldex.pm</strong> - obsoleted by the cpan module Text::Tidx. Sqldex may not actually be obsolete, because Tidx uses more ram and is slower for very small jobs. But for Exome and RNA-Seq work, <a href="http://search.cpan.org/%7Eearonesty/Text-Tidx/">Text::Tidx</a> beats both.</li> | |
| <li> | |
| <strong>qsh</strong> - Runs a bash script file like a "cluster aware makefile"...only processing newer things, dieing if things go wrong, and sending jobs to a queue manager if they're big. That way you don't have to write makefiles, or wrap things in "qsub" calls for every little program. Not really ready yet.</li> | |
| <li> | |
| <strong>grun</strong> - Fast, lightweight grid queue software. Keeps the job queue on disk at all times. Very fast. Works well by now</li> | |
| <li> | |
| <strong>gwrap</strong> - Bash wrapper shell that downloads all dependencies that are not the local system.... good for EC2 nodes. Linux only. Will use it if we ever go to EC2.</li> | |
| <li> | |
| <strong>gtf2bed</strong> - Converter that bundles up a GFF's exons and makes a UCSC-styled bed file with thin/thick properly set from the start/stop sites. </li> | |
| <li> | |
| <strong>randomFQ</strong> - takes a fastq (can be gzipped or paired-end) and randomly subsets to a user defined number of reads </li> | |
| </ul> | |
| <h1> | |
| <a id="citing" class="anchor" href="#citing" aria-hidden="true"><span class="octicon octicon-link"></span></a>Citing:</h1> | |
| <blockquote> | |
| <p>Erik Aronesty (2011). <em>ea-utils</em> : "Command-line tools for processing biological sequencing data"; <a href="https://github.com/ExpressionAnalysis/ea-utils">https://github.com/ExpressionAnalysis/ea-utils</a></p> | |
| <p>Erik Aronesty (2013). <em>TOBioiJ</em> : "Comparison of Sequencing Utility Programs", <a href="http://benthamscience.com/open/openaccess.php?tobioij/articles/V007/1TOBIOIJ.htm">DOI:10.2174/1875036201307010001</a></p> | |
| </blockquote> | |
| </section> | |
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| <p class="repo-owner"><a href="https://github.com/ExpressionAnalysis/ea-utils"></a> is maintained by <a href="https://github.com/ExpressionAnalysis">ExpressionAnalysis</a>.</p> | |
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