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ea-utils

command-line tools for processing biological sequencing data

Description

Ea-utils provides a set of 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.

Main Tools are:

 * fastq-mcf
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.
 * fastq-multx
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.
 * fastq-join
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.
 * varcall
Takes a pileup and calculates variants in a more easily parameterized manner than some other tools.

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Homepage

https://expressionanalysis.github.io/ea-utils/


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777 other people were interested in this package here. The newest known version of this software is 1.1.2+dfsg-5 (Information last updated about 1 hour ago.)