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{"name":"ea-utils","tagline":"FASTQ processing utilities","body":"# ea-utils has migrated to GitHub from https://code.google.com/p/ea-utils/\r\n# Overview: #\r\nCommand-line tools for processing biological sequencing data.  Barcode demultiplexing, adapter trimming, etc.\r\nPrimarily written to support an Illumina based pipeline - but should work with any FASTQs.\r\n  * **[fastq-mcf](https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMcf.md)** - 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.\r\n  * **[fastq-multx](https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMultx.md)** - 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.\r\n  * **[fastq-join](https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqJoin.md)** - 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.\r\n  * **[varcall](https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/Varcall.md)** - Takes a pileup and calculates variants in a more easily parameterized manner than some other tools.\r\n\r\n# Other Stuff: #\r\n  * **[sam-stats](https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/SamStats.md)** - Basic sam/bam stats.  Like other tools, but produces what I want to look at, in a format suitable for passing to other programs. \r\n  * **fastq-stats** - Basic fastq stats.  Counts duplicates. Option for per-cycle stats, or not (irrelevant for many sequencers). \r\n  * **determine-phred** - Returns the phred scale of the input file. Works with sams, fastq's or pileups and gzipped files.\r\n  * **Chrdex.pm** & **Sqldex.pm** - 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, [Text::Tidx](http://search.cpan.org/~earonesty/Text-Tidx/) beats both.\r\n  * **qsh** - 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.\r\n  * **grun** - Fast, lightweight grid queue software.  Keeps the job queue on disk at all times.  Very fast.   Works well by now\r\n  * **gwrap** - 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.\r\n  * **gtf2bed** - 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. \r\n  * **randomFQ** - takes a fastq (can be gzipped or paired-end) and randomly subsets to a user defined number of reads \r\n\r\n# Citing: #\r\n> Erik Aronesty (2011). _ea-utils_ : \"Command-line tools for processing biological sequencing data\"; https://github.com/ExpressionAnalysis/ea-utils\r\n\r\n> Erik Aronesty (2013). _TOBioiJ_ : \"Comparison of Sequencing Utility Programs\", [DOI:10.2174/1875036201307010001](http://benthamscience.com/open/openaccess.php?tobioij/articles/V007/1TOBIOIJ.htm)","google":"","note":"Don't delete this file! It's used internally to help with page regeneration."}