SQT

NAME

sqt - SeQuencing Tools for biological DNA/RNA high-throughput data

DESCRIPTION

usage: sqt [-h] [--version]

{align, bam2fastq, fastxmod, qgramfreq, chars, fastagrep, readcov, randomseq, samsetop, bameof, readlenhisto, cutvect} ...

SeQuencing Tools -- command-line tools for working with sequencing data

positional arguments:

{align, bam2fastq, fastxmod, qgramfreq, chars, fastagrep, readcov, randomseq, samsetop, bameof, readlenhisto, cutvect}

align

Compare two strings

bam2fastq

Extract all reads from a BAM file that map to a certain location, but try hard

fastxmod

Modify FASTA and FASTQ files by picking subsets and modifying individual entries.

qgramfreq

Print q-gram (also called k-mer) frequencies in a FASTA or FASTQ file.

chars

Print the number of characters in a string.

fastagrep

Search for a IUPAC string in the sequences of a FASTA file.

readcov

Print a report for individual reads in a SAM/BAM file.

randomseq

Generate random sequences in FASTA format

samsetop

Perform set operation on two SAM/BAM files.

bameof

Check whether the EOF marker is present in BAM files.

readlenhisto

Print and optionally plot a read length histogram of one or more FASTA or FASTQ

cutvect

Remove vector sequence

optional arguments:

-h, --help

show this help message and exit

--version

show program’s version number and exit

AUTHOR

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