fastq-utils - Fastq Utilities

Overview

Commands

  • Interleave/deinterleave paired-end fastq files.

  • Converts to FASTA

  • sort 2 files to sync the headers

Changes

Changed in version 0.3.4: moved to use click, internal fastq parsing, removed rand command

Changed in version 0.3.1: added stdin/stdout defaults for some commands

Changed in version 0.3.0: added convert command to FASTA

Options

fastq-utils

Main function

fastq-utils [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

--cite

convert

Convert FastQ file [fastq-file] to FASTA file [fasta-file]

fastq-utils convert [OPTIONS] [FASTQ_FILE] [FASTA_FILE]

Options

-v, --verbose

Arguments

FASTQ_FILE

Optional argument

FASTA_FILE

Optional argument

di

Deinterleave sequences from [fastq-file], into [mate1-file] and [mate2-file]

fastq-utils di [OPTIONS] [FASTQ_FILE] MATE1_FILE MATE2_FILE

Options

-v, --verbose
-s, --strip

Strip additional info

Arguments

FASTQ_FILE

Optional argument

MATE1_FILE

Required argument

MATE2_FILE

Required argument

il

Interleave sequences from [mate1-file] and [mate2-file] into [fastq-file]

fastq-utils il [OPTIONS] MATE1_FILE MATE2_FILE [FASTQ_FILE]

Options

-v, --verbose

Arguments

MATE1_FILE

Required argument

MATE2_FILE

Required argument

FASTQ_FILE

Optional argument

sort

Sort paired-end sequences from [mate1-input] and [mate2-input] into files [mate1-output] and [mate2-output]

fastq-utils sort [OPTIONS] MATE1_INPUT MATE2_INPUT MATE1_OUTPUT MATE2_OUTPUT

Options

-v, --verbose

Arguments

MATE1_INPUT

Required argument

MATE2_INPUT

Required argument

MATE1_OUTPUT

Required argument

MATE2_OUTPUT

Required argument