Balík: spades (3.15.5+dfsg-8)

[ Zdroj: 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).

Značky: Biológia: Nucleic Acids, Pole: Biológia, field::biology:bioinformatics, implemented-in::c++, Implementované v: Python, User Interface: interface::commandline, role::program, Scope: Utility, Works with: works-with::biological-sequence, works-with::file

Ostatné balíky súvisiace s balíkom spades

• dep: bamtools

  toolkit for manipulating BAM (genome alignment) files

• dep: bwa

  Burrows-Wheeler Aligner

• dep: libc6 (>= 2.38)

  knižnica GNU C - zdieľané knižnice
  tiež virtuálny balík poskytovaný balíkom libc6-udeb

• dep: libgcc-s1 (>= 4.0)

  podporná knižnica GCC

• dep: libgomp1 (>= 6)

  podporná knižnica GCC OpenMP (GOMP)

• dep: libnlopt0 (>= 2.6.1)

  nonlinear optimization library

• dep: libssw0 (>= 1.1)

  fast SIMD parallelized implementation of the Smith-Waterman algorithm

• dep: libstdc++6 (>= 14)

  štandardná knižnica C++ GNU v3

• dep: python3

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

• dep: python3-joblib

  nástroje na nenáročnú tvorbu rúr v jazyku Python

• dep: python3-packaging

  základné nástroje balíkov jazyka Python 3

• dep: python3-yaml

  spracovanie a tvorbu YAML v jazyku Python 3

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• dep: zlib1g (>= 1:1.2.3.3)

  komprimačná knižnica - dynamická verzia

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Stiahnuť pre všetky dostupné architektúry

Architektúra	Veľkosť balíka	Nainštalovaná veľkosť	Súbory
amd64	9,012.5 kB	39,888.0 kB	[zoznam súborov]