sqt - SeQuencing Tools for biological DNA/RNA high-throughput
data
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
- {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
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.