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.