Paquet : python3-sqt (0.8.0-8 et autres) [debports]

[ Paquet source :  ]

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.

Autres paquets associés à python3-sqt

• dep: libc6.1 (>= 2.4)

  bibliothèque C GNU : bibliothèques partagées
  un paquet virtuel est également fourni par libc6.1-udeb

• dep: python3

  langage orienté objet interactif de haut niveau – version par défaut de Python 3

  dep: python3 (<< 3.13)

  dep: python3 (>= 3.12~)

• dep: python3-cutadapt

  Clean biological sequences from high-throughput sequencing reads (Python 3)

• dep: python3-matplotlib

  système de traçage basé sur Python dans un style similaire à celui Matlab

• dep: python3-pysam

  interface for the SAM/BAM sequence alignment and mapping format (Python 3)

• dep: python3-seaborn

  bibliothèque de visualisation de statistiques pour Python 3

• dep: python3-xopen

  Python3 module to open compressed files transparently

• rec: fonts-noto-color-emoji

  fonte colorée d’émoticônes de Google

Télécharger python3-sqt

Télécharger pour toutes les architectures proposées

Architecture	Version	Taille du paquet	Espace occupé une fois installé	Fichiers
alpha (portage non officiel)	0.8.0-8+b1	123,3 ko	477,0 ko	[liste des fichiers]