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fastq-mcf

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

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 it does skewing detection and quality filtering; detects levels of adapter presence, computes likelihoods and locations (start, end) of the adapters; removes the adapter sequences from the fastq file(s). More specifically, fastq-mcf attempts to: detect & remove sequencing adapters and primers; detect limited skewing at the ends of reads and clip; detect poor quality at the ends of reads and clip; detect Ns, and remove from ends; remove reads with CASAVA *Y* flag (purity filtering); discard sequences that are too short after all of the above; keep multiple mate-reads in sync while doing all of the above. Importantly, to turn off adapter trimming user must specify n or a. This is instead of providing a input file with adapters (a simple fasta formatted file)


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.