Ray Assembly¶

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. As our AWS instance has 16 cores, we specify this in the `mpiexec -n 16 ` command to let Ray know it should use 16 parallel MPI processes:

cd /vol/spool/tutorial-data
mpiexec -n 16 Ray -k 31 -p read1.fq read2.fq -o ray_31 >& ray_31.log &

This will create the output directory ray_31 and the final contigs are located in ray_31/Contigs.fasta. Again, let’s get some basic statistics on the contigs:

getN50.pl -s 500 -f ray_31/Contigs.fasta

Now 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/tutorial-data
./get_assembly_stats.sh

Note

Most jobs above will be started in the backgroud using the & at the end of each command, which allows you to continue working in the shell.

You can watch your running jobs by typing top (hit q to exit top).

You can look into the log-files by typing e.g. less LOGFILE (hit q to quit) or tail -f LOGFILE (hit ^C to quit).