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fastq-multx

By Aronesty E., Last update 1494698998
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fastq-multx description

Fastq-multix demultiplexes a fastq file. 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. The idea behind this is to reduce the amount of 'piping' going on in a pipeline. A lot of time, disk space and nail-chewing is spent keeping files in sync, figuring out what barcodes are on what samples, etc. The goal of this program is to make it easier to demultiplex possibly paired-end sequences, and also to allow the 'guessing' of barcode sets based on master lists of barcoding protocols (fluidigm, truseq, etc.). Fasta-formatted file with barcodes can also be specified to do demultiplexing


Parent program: ea-utils

Ea-utils is FASTQ processing utilities such as fastq-mcf, fastq-multx, fastq-join, varcall and sam-stats and other. These tools detect and remove sequencing adapters and primers, detect limited skewing at the ends of reads and clip, poor quality at the ends of reads and clip, discard sequences that are too short after all of the above, keep multiple mate-reads in sync while doing all of the above, merge overlapping paired-end reads and computing statisticsfrom SAM, BAM or Fasta files.