TO_FASTA.PY

NAME

to_fasta.py - Remove adapters and collapse reads from FASTQ to FASTA

DESCRIPTION

usage: to_fasta.py [-h] [-3 SEQ] [-5 SEQ] [--trim-5p BP] [--trim-3p BP]

[--seed-5p BP] [--seed-3p BP] [-m BP] [-x BP] [-s] [-B] [-a] FASTQ

Remove adapters and collapse reads from FASTQ to FASTA

positional arguments:

FASTQ

including stdin or compressed file {zip,gz,tar,bz}

optional arguments:

-h, --help

show this help message and exit

-3 SEQ

3’adapter sequence

-5 SEQ

5’adapter sequence

--trim-5p BP

trim specified number of bases from 5’ends

--trim-3p BP

trim specified number of bases from 3’ends

--seed-5p BP

5’ adapter match length in bp (default: 7)

--seed-3p BP

3’ adapter match length in bp (default: 7)

	-m BP		minimum read length in bp (default: 16)
	-x BP		maximum read length in bp (default: 36)
	-s		sensitive adapter search with 1 mismatch (default: off)
	-B		only print the reads with both 5’ and 3’ adapter matches
	-a		print all reads with and without adapter matches if the reads are in the range specified with ’-m’ and ’-x’

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.