Пакунок: spades (4.0.0+dfsg1-1)

Links for spades

Debian Resources:

Download Source Package spades:

Maintainers:

Debian Med Packaging Team (QA Page, Mail Archive)
Andreas Tille (QA Page)
Sascha Steinbiss (QA Page)
Michael R. Crusoe (QA Page)
Alexandre Mestiashvili (QA Page)
Étienne Mollier (QA Page)

External Resources:

Homepage [github.com]

Similar packages:

Експериментальний пакунок

Warning: This package is from the experimental distribution. That means it is likely unstable or buggy, and it may even cause data loss. Please be sure to consult the changelog and other possible documentation before using it.

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

Інші пакунки пов'язані з spades

depends

recommends

suggests

enhances

dep: bamtools

toolkit for manipulating BAM (genome alignment) files
dep: bwa

Burrows-Wheeler Aligner
dep: libbamtools2.5.2 (>= 2.5.2+dfsg)

dynamic library for manipulating BAM (genome alignment) files
dep: libc6 (>= 2.38)

Бібліотека GNU C: спільні бібліотеки
also a virtual package provided by libc6-udeb
dep: libgcc-s1 (>= 4.0)

Допоміжна бібліотека GCC
dep: libgomp1 (>= 6)

Підтримувальна бібліотека GCC OpenMP (GOMP)
dep: libnlopt0 (>= 2.6.1)

nonlinear optimization library
dep: libspoa7.0.0 (>= 4.0.5)

SIMD partial order alignment library
dep: libssw0 (>= 1.1)

fast SIMD parallelized implementation of the Smith-Waterman algorithm
dep: libstdc++6 (>= 14)

Стандартна бібліотека C++ GNU, версії 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

основні утиліти для пакунків python3
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)

Бібліотека стискання даних (виконавчий модуль)

Завантажити spades

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Архітектура	Розмір пакунка	Розмір після встановлення	Файли
amd64	7,872.8 kB	46,657.0 kB	[список файлів]