SPAdes

What is SPAdes?

SPAdes, or St. Petersburg genome assembler, is a genome pipeline developed by St. Petersburg's Center for Algorithmic Biotechnology to assist with the genomic endeavors.

How is SPAdes loaded?

The below can be used to view all of the installations of SPAdes on a particular system, where this example uses Coeus.

$ module avail |& grep -i "spades"

Biosciences/spades/3.11.1/gcc

How is SPAdes invoked?

To invoke SPAde's primary binary, use the below. For more on using SPAdes, refer to here.

$ module load Biosciences/bwa/0.7.12/gcc-7.2.0

$ spades

$ # or

$ python3 spades.py

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