Пакет: spades (3.15.5+dfsg-2)

[ Източник: 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).

Етикети: Biology: Nucleic Acids, Field: Biology, field::biology:bioinformatics, implemented-in::c++, Implemented in: Питон, User Interface: interface::commandline, role::program, Scope: Utility, Works with: works-with::biological-sequence, works-with::file

Други пакети, свързани с spades

• dep: bamtools

  toolkit for manipulating BAM (genome alignment) files

• dep: bwa

  Burrows-Wheeler Aligner

• dep: libc6 (>= 2.34)

  GNU C Library: Shared libraries
  също и виртуален пакет, предлаган от libc6-udeb

• dep: libgcc-s1 (>= 4.0)

  GCC support library

• dep: libgomp1 (>= 6)

  GCC OpenMP (GOMP) support library

• dep: libnlopt0 (>= 2.6.1)

  nonlinear optimization library

• dep: libssw0 (>= 1.1)

  fast SIMD parallelized implementation of the Smith-Waterman algorithm

• dep: libstdc++6 (>= 12)

  GNU Standard C++ Library v3

• dep: python3

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

• dep: python3-distutils

  distutils package for Python 3.x

• dep: python3-joblib

  tools to provide lightweight pipelining in Python

• dep: python3-yaml

  YAML parser and emitter for Python3

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• dep: zlib1g (>= 1:1.2.3.3)

  compression library - runtime

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