.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH TO_FASTA.PY "1" "March 2020" "to_fasta.py 1.1" "User Commands"
.SH NAME
to_fasta.py \- Remove adapters and collapse reads from FASTQ to FASTA
.SH DESCRIPTION
usage: to_fasta.py [\-h] [\-3 SEQ] [\-5 SEQ] [\-\-trim\-5p BP] [\-\-trim\-3p BP]
.IP
[\-\-seed\-5p BP] [\-\-seed\-3p BP] [\-m BP] [\-x BP] [\-s] [\-B]
[\-a]
FASTQ
.PP
Remove adapters and collapse reads from FASTQ to FASTA
.SS "positional arguments:"
.TP
FASTQ
including stdin or compressed file {zip,gz,tar,bz}
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-3\fR SEQ
3'adapter sequence
.TP
\fB\-5\fR SEQ
5'adapter sequence
.TP
\fB\-\-trim\-5p\fR BP
trim specified number of bases from 5'ends
.TP
\fB\-\-trim\-3p\fR BP
trim specified number of bases from 3'ends
.TP
\fB\-\-seed\-5p\fR BP
5' adapter match length in bp (default: 7)
.TP
\fB\-\-seed\-3p\fR BP
3' adapter match length in bp (default: 7)
.TP
\fB\-m\fR BP
minimum read length in bp (default: 16)
.TP
\fB\-x\fR BP
maximum read length in bp (default: 36)
.TP
\fB\-s\fR
sensitive adapter search with 1 mismatch (default: off)
.TP
\fB\-B\fR
only print the reads with both 5' and 3' adapter matches
.TP
\fB\-a\fR
print all reads with and without adapter matches if the reads
are in the range specified with '\-m' and '\-x'
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.