Paket: spades (3.15.5+dfsg-8)

[ Quellcode: spades  ]

genome assembler for single-cell and isolates data sets

The SPAdes – St. Petersburg genome assembler is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio and Sanger reads. You can also provide additional contigs that will be used as long reads.

This package provides the following additional pipelines:

 * metaSPAdes – a pipeline for metagenomic data sets
 * plasmidSPAdes – a pipeline for extracting and assembling plasmids
   from WGS data sets
 * metaplasmidSPAdes – a pipeline for extracting and assembling
   plasmids from metagenomic data sets
 * rnaSPAdes – a de novo transcriptome assembler from RNA-Seq data
 * truSPAdes – a module for TruSeq barcode assembly
 * biosyntheticSPAdes – a module for biosynthetic gene cluster
   assembly with paired-end reads

SPAdes provides several stand-alone binaries with relatively simple command-line interface: k-mer counting (spades-kmercounter), assembly graph construction (spades-gbuilder) and long read to graph aligner (spades-gmapper).

Markierungen: Biologie: Nukleinsäuren, Feld: Biologie, field::biology:bioinformatics, implemented-in::c++, Implementiert in: Python, Benutzer-Schnittstellen: interface::commandline, role::program, Zweck: Hilfswerkzeug, Arbeitet mit: works-with::biological-sequence, works-with::file

Andere Pakete mit Bezug zu spades

• dep: bamtools

  toolkit for manipulating BAM (genome alignment) files

• dep: bwa

  Burrows-Wheeler Aligner

• dep: libc6 (>= 2.38)

  GNU-C-Bibliothek: Laufzeitbibliotheken
  auch ein virtuelles Paket, bereitgestellt durch libc6-udeb

• dep: libgcc-s1 (>= 4.0)

  GCC Support-Bibliothek

• dep: libgomp1 (>= 6)

  Unterstützungsbibliothek für GCC OpenMP (GOMP)

• dep: libnlopt0 (>= 2.6.1)

  Bibliothek für nichtlineare Optimierung

• dep: libssw0 (>= 1.1)

  fast SIMD parallelized implementation of the Smith-Waterman algorithm

• dep: libstdc++6 (>= 14)

  GNU-Implementierung der Standard-C++-Bibliothek (Version 3)

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: python3-joblib

  tools to provide lightweight pipelining in Python

• dep: python3-packaging

  Kern-Dienstprogramme für Python3-Pakete

• dep: python3-yaml

  Python3-Parser und -Emitter für YAML

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• dep: zlib1g (>= 1:1.2.3.3)

  Kompressions-Bibliothek - Laufzeit

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