deb_control_files:
- control
- md5sums
- postinst
- prerm
deb_fields:
Architecture: amd64
Depends: libc6 (>= 2.14), python3 (<< 3.14), python3 (>= 3.12~), python3-cutadapt,
python3-matplotlib, python3-pysam, python3-seaborn, python3-xopen, python3:any
Description: |-
SeQuencing Tools for biological DNA/RNA high-throughput data
sqt is a collection of command-line tools for working with
high-throughput sequencing data. Conceptionally not fixed to use any
particular language, many sqt subcommands are currently implemented
in Python. For them, a Python package is available with functions for
reading and writing FASTA/FASTQ files, computing alignments, quality
trimming, etc.
.
The following tools are offered:
* sqt-coverage -- Compute per-reference statistics such as coverage
and GC content
* sqt-fastqmod -- FASTQ modifications: shorten, subset, reverse
complement, quality trimming.
* sqt-fastastats -- Compute N50, min/max length, GC content etc. of
a FASTA file
* sqt-qualityguess -- Guess quality encoding of one or more FASTA files.
* sqt-globalalign -- Compute a global or semiglobal alignment of two strings.
* sqt-chars -- Count length of the first word given on the command line.
* sqt-sam-cscq -- Add the CS and CQ tags to a SAM file with colorspace reads.
* sqt-fastamutate -- Add substitutions and indels to sequences in a
FASTA file.
* sqt-fastaextract -- Efficiently extract one or more regions from an
indexed FASTA file.
* sqt-translate -- Replace characters in FASTA files (like the 'tr'
command).
* sqt-sam-fixn -- Replace all non-ACGT characters within reads in a
SAM file.
* sqt-sam-insertsize -- Mean and standard deviation of paired-end
insert sizes.
* sqt-sam-set-op -- Set operations (union, intersection, ...) on
SAM/BAM files.
* sqt-bam-eof -- Check for the End-Of-File marker in compressed
BAM files.
* sqt-checkfastqpe -- Check whether two FASTQ files contain correctly
paired paired-end data.
Homepage: https://bitbucket.org/marcelm/sqt
Installed-Size: '664'
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Package: python3-sqt
Priority: optional
Recommends: fonts-noto-color-emoji
Section: python
Source: python-sqt (0.8.0-8)
Version: 0.8.0-8+b2
srcpkg_name: python-sqt
srcpkg_version: 0.8.0-8