Package: python3-sqt
Source: python-sqt
Version: 0.8.0-9
Architecture: arm64
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 474
Depends: libc6 (>= 2.17), python3 (<< 3.14), python3 (>= 3.13~), python3-cutadapt, python3-matplotlib, python3-pysam, python3-seaborn, python3-xopen, python3:any
Recommends: fonts-noto-color-emoji
Section: python
Priority: optional
Homepage: https://bitbucket.org/marcelm/sqt
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.
