recipe spades

SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.

Homepage:

http://cab.spbu.ru/software/spades/

Documentation:

http://cab.spbu.ru/files/release3.15.5/manual.html

Developer docs:

https://github.com/ablab/spades

License:

GPL / GPLv2

Recipe:

/spades/meta.yaml

Links:

biotools: spades, usegalaxy-eu: spades, doi: 10.1089/cmb.2012.0021, doi: 10.1101/gr.213959.116, doi: 10.1093/gigascience/giz100, doi: 10.1093/bioinformatics/btz349

SPAdes (St. Petersburg genome assembler) is a genome assembly algorithm which was designed for single cell and multi-cells bacterial data sets. However, it might not be suitable for large genomes projects.

SPAdes works with Ion Torrent, PacBio, Oxford Nanopore, and Illumina paired-end, mate-pairs and single reads

package spades

Versions:

3.15.5-1,  3.15.5-0,  3.15.4-0,  3.15.3-1,  3.15.3-0,  3.15.2-1,  3.15.2-0,  3.15.0-0,  3.14.1-2, 

3.15.5-1,  3.15.5-0,  3.15.4-0,  3.15.3-1,  3.15.3-0,  3.15.2-1,  3.15.2-0,  3.15.0-0,  3.14.1-2,  3.14.1-1,  3.14.1-0,  3.14.0-0,  3.13.2-0,  3.13.1-2,  3.13.1-1,  3.13.1-0,  3.13.0-0,  3.12.0-3,  3.12.0-2,  3.12.0-1,  3.12.0-0,  3.11.1-5,  3.11.1-4,  3.11.1-3,  3.11.1-2,  3.11.1-1,  3.11.1-0,  3.11.0-1,  3.11.0-0,  3.10.1-1,  3.10.1-0,  3.10.0-0,  3.9.1-1,  3.9.1-0,  3.9.0-4,  3.9.0-3,  3.9.0-2,  3.9.0-1,  3.9.0-0,  3.8.1-0,  3.8.0-0,  3.7.0-0,  3.6.2-0,  3.5.0-1,  3.5.0-0

Depends:

• bzip2 >=1.0.8,<2.0a0

• libgcc-ng >=12

• libstdcxx-ng >=12

• libzlib >=1.2.12,<1.3.0a0

• openmp

• python

• sysroot_linux-64 2.17.*

Required By:

• aquilasv

• metasv

• asqcan

• markermag

• phyloflash

• secapr

• milonga

• haphpipe

• plascope

• getorganelle

• proksee

• datma

• seqsero2

• ariba

• plasmidtron

• mitgard

• zga

• riboseed

• mitoz

• metawrap-mg

• bttoxin_digger

• etoki

• tetyper

• itero

• hybpiper

• circlator

• shovill-se

• mitofinder

• anvio

• plasmidid

• fargene

• vsnp3

• unicycler

• nullarbor

• tritimap

• shovill

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install spades

and update with:

conda update spades

or use the docker container:

docker pull quay.io/biocontainers/spades:<tag>

(see spades/tags for valid values for <tag>)

Download stats

Link to this page

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