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blt fastq-derep.sh(1) General Commands Manual blt fastq-derep.sh(1) SYNOPSIS blt fastq-derep.sh file.fastq|fq[.xz|.bz2|.gz] ARGUMENTS filename FASTQ file optionally compressed with xz, bzip2, or gzip DESCRIPTION blt fastq-derep.sh removes replicates from a fastq file using fastq2tsv to reformat to tab-separated data for easier sorting, then using Unix sort and an awk script to remove adjacent entries with the same se- quence (column 2 of the TSV). Per latest benchmarks, seqkit rmdup --by-sequence and our own C version, blt fastq-derep, are about 3x as fast. However, blt fastq-derep.sh does not require the entire file in memory as it uses the Unix sort command, which automatically breaks large files into chunks for later merging. EXAMPLES blt fastq-derep.sh file.fastq.xz SEE ALSO blt-fastx2tsv(1), blt-fastx-derep(1) AUTHOR J. Bacon blt fastq-derep.sh(1)
SYNOPSIS | ARGUMENTS | DESCRIPTION | EXAMPLES | SEE ALSO | AUTHOR
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