---
name: "sqt"
section: "1"
platform: "linux"
package: "python3-sqt"
version: "0.8.0-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sqt"
---

# sqt(1)

SeQuencing Tools for biological DNA/RNA high-throughput data

## 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.