spades


Introduction:

SPADES is an assembly toolkit containing various assembly pipelines.

SPADES works with Illumina or IonTorrent reads, and is capable of
providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger
reads. You can also provide additional contigs that will be used as
long reads.

SPADES supports paired-end reads, mate-pairs and unpaired reads. It
can take as input several paired-end and mate-pair libraries
simultaneously. SPADES was initially designed for small genomes. It
was tested on bacterial (both single-cell MDA and standard isolates),
fungal and other small genomes. SPADES is not intended for larger
genomes, such as mammalian size genomes. For such purposes, you
use SPADES at your own risk.

Web Site:

The SPADES home page at St Petersburg state university:

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

Reference:

Usage:

On any ARC cluster, check the installation details
by typing “module spider spades”.

SPADES requires that the appropriate modules be loaded before it can
be used. One version of the appropriate commands for use on NewRiver is:

module purge
module load gcc/5.2.0
module load spades/3.6.0
    

Examples:

The following batch file demonstrates the use of SPADES:

#! /bin/bash
#
#PBS -l walltime=0:05:00
#PBS -l nodes=1:ppn=1
#PBS -W group_list=newriver
#PBS -q open_q
#PBS -j oe
#
cd $PBS_O_WORKDIR
#
module purge
module load gcc/5.2.0
module load spades/3.6.0
#
python $SPADES_BIN/spades.py --test

A complete set of files to carry out a similar process are available in
spades_example.tar