SPAdes
Contents
Introduction
Pavel Pevzner's de-novo assembler, primarily for - but not restricted to - prokaryotes.
I uses Bayeshammer[1] 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
Outputs
The outputs from a SPAdes run
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.
