fgbio

Tools for working with genomic and high throughput sequencing data.

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SortFastq

Overview

Group: FASTQ

Sorts a FASTQ file. Sorts the records in a FASTQ file based on the lexicographic ordering of their read names. Input and output files can be either uncompressed or gzip-compressed.

Arguments

Name Flag Type Description Required? Max # of Values Default Value(s)
input i PathToFastq Input fastq file. Required 1  
output o PathToFastq Output fastq file. Required 1  
max-records-in-ram m Int Maximum records to keep in RAM at one time. Optional 1 500000