SPAdes

Introduction

Pavel Pevzner's de-novo assembler, primarily for - but not restricted to - prokaryotes.

I uses Bayeshammer to correct errors.

Usage

A basic SPAdes run for a pair of fastq's would use their python script (extension .py) in the following manner:

spades.py -o <output_directoryname> --pe1-1 <first_of_pair_fastq> --pe1-2 <second_of_pair_fastq>

NOTE: SPAdes' output files have generic names, so when running on several fastq samples it is essential that the output be directed to uniquely named directories.

Note that:

• SPAdes has a nanopore option.
• metaspades.py is for metagenome assembly. It is the same as spades.py --meta
• SPAdes uses python as a wrapping tool, so it uses the system python and not bulked-up python in the modules system, due to its not needing any special libraries.

Outputs

The outputs from a SPAdes run:

Files:

• assembly_graph.fastg
• assembly_graph.gfa
• before_rr.fasta
• contigs.paths
• dataset.info, simply refers to the yaml file.
• first_pe_contigs.fasta
• input_dataset.yaml, simply
• params.txt
• scaffolds.paths
• spades.log
• contigs.fasta, final contigs
• scaffolds.fasta, final scaffolds, this means the final assembly, mostly. Preferred over the contigs.fasta.

Folders:

• corrected
• K21
• K33
• K55
• tmp
• misc

Example qsub job script

#!/bin/bash
#$ -cwd 
#$ -j y
#$ -S /bin/bash 
#$ -V
#$ -q unstable.q
#$ -pe multi 16

# some quick "argument accounting"
EXPECTED_ARGS=1 # change value to suit!
if [ $# -ne $EXPECTED_ARGS ]; then
    echo "error, this script should be fed with one argument: a filelist of fastq(.gz) files"
    exit
fi
module load SPAdes
N=( $(cat $1) )
NSZ=${#N[@]}
for((i=2; i<NSZ; i+=2)); do
    R1=${N[$i]}
    R2=${N[$(($i+1))]}
    ON=${N[$i]%%_*}
    # echo "spades.py -t 6 -o $ON --pe1-1 $R1 --pe1-2 $R2"
    spades.py -t $NSLOTS -o $ON --pe1-1 $R1 --pe1-2 $R2
done

Output

The output directory defined in the SPAdes command line will contain the following key elements:

• the corrected subdirectory containing fastq reads corrected by BayesHammer.
• the contigs.fasta file containing the resulting contigs.
• the scaffolds.fasta file containing the resulting scaffolds.
• the assembly_graph.fastg file containing the SPAdes assembly graph in FASTG format
• the contigs.paths file containing paths in the assembly graph corresponding to contigs.fasta file mentioned above.
• the scaffolds.paths file: similar to contigs.path except with the scaffold paths as its name suggests.

Installation (Sysadmin notes)

Initially version 3.7.0 was installed using the specially compiled gcc/4.9.3 compiler (available as a module). However the -b version of the module now uses Redhat's devtoolset-2, so that this compiler is not necessary.

Boost however, is necessary. The cluster has the latest version: 1.60. Possibly compiled (well, the bits that can be compiled) with g++ 4.4.7. In any case, the location of boost is a problem, although the boost module on the cluster does create some useful environmental variables, the given stacks_compile script does recognise them.

In any case, the configure system is cmake, so a "build" subdirectory should be created. Inside that, a short compile script containing something like the following should be created:

module load boost
cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=.. -DBoost_NO_BOOST_CMAKE=TRUE -DBoost_NO_SYSTEM_PATHS=TRUE -DBOOST_ROOT:PATHNAME=${BOOST_ROOT} -DBoost_INCLUDE_DIRS:FILEPATH=${BOOST_INCLUDEDIR} -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_LIBRARYDIR} ../src

There is no make test nor make check before installation. Post-installation, however, there is a test script in the installation (not the source) directory, whihc can be invoked as follows:

<spades installation dir>/spades.py --test

or

<spades installation dir>/truspades.py --test

For the truspades modality.

Links

• Official manual

http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-S1-S7