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Demultiplexes a fastq.
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recipe bumps version Jan 24, 2017
tests init Dec 15, 2015
Makefile g++ Dec 15, 2015 Update Mar 29, 2018
fastq-lib.cpp init Dec 15, 2015
fastq-lib.h init Dec 15, 2015
fastq-multx.cpp bumps version Jan 24, 2017


This is the work of:

Erik Aronesty (2013). TOBioiJ : "Comparison of Sequencing Utility Programs", DOI:10.2174/1875036201307010001


The Versioning here is awful. I've bumped the version with no alterations to the original algorithm of Erik.


git clone
cd fastq-multx

Sequences are sometimes output to STDOUT in a different order on OS X versus Redhat, therefore some tests may fail.

Example Usage

fastq-multx -B barcodes.tsv -m 0 \
    Undetermined_S0_L001_I1_001.fastq.gz \
    Undetermined_S0_L001_R1_001.fastq.gz \
    Undetermined_S0_L001_R2_001.fastq.gz \
    -o n/a -o %_R1.fastq -o %_R2.fastq
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