SPAdes

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Description

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

Availability

Versions 3.1.0, 3.6.0, 3.9.0, 3.11.1 and 3.13.0

From version 3.9.0 includes a de novo transcriptome assembler from RNA-Seq data (rnaSPAdes)

Use

module add spades-3.13.0
spades.py

or

rnaspades.py

In qsub command specify parameter ompthreads to allow run on multiple threads, e.g. (for 16 threads run)

qsub -l select=1:ncpus=16:ompthreads=16:mem=

Documentation

http://spades.bioinf.spbau.ru/release3.6.0/manual.html http://spades.bioinf.spbau.ru/release3.9.0/manual.html http://spades.bioinf.spbau.ru/release3.9.1/rnaspades_manual.html

Licence

GPL version 2.

Program manager

meta@cesnet.cz

Homepage

http://bioinf.spbau.ru/en/spades