.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH SQT "1" "January 2019" "sqt 0.8.0" "User Commands"
.SH NAME
sqt \- SeQuencing Tools for biological DNA/RNA high-throughput data
.SH DESCRIPTION
usage: sqt [\-h] [\-\-version]
.IP
{align,bam2fastq,fastxmod,qgramfreq,chars,fastagrep,readcov,randomseq,samsetop,bameof,readlenhisto,cutvect}
\&...
.PP
SeQuencing Tools \fB\-\-\fR command\-line tools for working with sequencing data
.SS "positional arguments:"
.IP
{align,bam2fastq,fastxmod,qgramfreq,chars,fastagrep,readcov,randomseq,samsetop,bameof,readlenhisto,cutvect}
.TP
align
Compare two strings
.TP
bam2fastq
Extract all reads from a BAM file that map to a
certain location, but try hard
.TP
fastxmod
Modify FASTA and FASTQ files by picking subsets and
modifying individual entries.
.TP
qgramfreq
Print q\-gram (also called k\-mer) frequencies in a
FASTA or FASTQ file.
.TP
chars
Print the number of characters in a string.
.TP
fastagrep
Search for a IUPAC string in the sequences of a FASTA
file.
.TP
readcov
Print a report for individual reads in a SAM/BAM file.
.TP
randomseq
Generate random sequences in FASTA format
.TP
samsetop
Perform set operation on two SAM/BAM files.
.TP
bameof
Check whether the EOF marker is present in BAM files.
.TP
readlenhisto
Print and optionally plot a read length histogram of
one or more FASTA or FASTQ
.TP
cutvect
Remove vector sequence
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR
show program's version number and exit
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.