Package: spades (3.15.5+dfsg-7)

[ Source: 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).

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

Other Packages Related to spades

• dep: bamtools

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• dep: bwa

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• dep: libc6 (>= 2.34)

  GNU C könyvtár: megosztott könyvtárak
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• dep: libgcc-s1 (>= 4.0)

  GCC támogató programkönyvtár

• dep: libgomp1 (>= 6)

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• dep: libnlopt0 (>= 2.6.1)

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• dep: libssw0 (>= 1.1)

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• dep: libstdc++6 (>= 13.1)

  GNU Standard C++ Library v3

• dep: python3

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

• dep: python3-joblib

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• dep: python3-packaging

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• dep: python3-yaml

  YAML parser and emitter for Python3

• dep: samtools

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• dep: zlib1g (>= 1:1.2.3.3)

  tömörítő könyvtár - futásidejű

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Architecture	Package Size	Installed Size	Files
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