Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data. Ray is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard. See the Ray home page for more info.
Ray can be run by the following command using a kmer-length of 31 and 51, repectively. As our compute instance have multiple cores, we specify this in the mpiexec -n 14 command to let Ray know it should use 14 parallel MPI processes:
cd /vol/spool/workdir/assembly/
qsub -cwd -pe multislot 14 -N ray -b y \
/usr/bin/mpiexec -n 14 /usr/bin/Ray -k 31 -p read1.fq read2.fq -o ray_31
qsub -cwd -pe multislot 14 -N ray -b y \
/usr/bin/mpiexec -n 14 /usr/bin/Ray -k 51 -p read1.fq read2.fq -o ray_51This will create the output directory ray_31 and ray_51 the final contigs are located in ray_31/Contigs.fasta and ray_51/Contigs.fasta. Again, let's get some basic statistics on the contigs:
getN50.pl -s 500 -f ray_31/Contigs.fasta
getN50.pl -s 500 -f ray_51/Contigs.fastaNow that you have run assemblies using Velvet, MEGAHIT, IDBA-UD and Ray, let's have a quick look at the assembly statistics of all of them:
cd /vol/spool/workdir/assembly/
./get_assembly_stats.sh