Running itero

itero has both a local mode and an MPI mode. The local mode is for execution on a single node, while the MPI mode executes individual locus assemblies in parallel using an MPI-enabled HPC cluster. To run the program, you must first create a configuration file denoting the samples you wish you assemble. That file has the following format:

[reference]
/path/to/the/locus/seeds.fasta

[individuals]
taxon-one:/path/to/fastq/R1/and/R2/files/for/taxon/1/
taxon-two:/path/to/fastq/R1/and/R2/files/for/taxon/2/
taxon-three:/path/to/fastq/R1/and/R2/files/for/taxon/3/

itero on a single node

You then run the local version using a command similar to:

itero assemble local --config ndna-test.conf
    --output local
    --local-cores 16
    --iterations 6

This will run itero on a single node and will first use 16 cores to perform bwa alignments. The code will then distribute locus-specific assemblies across all cores on the node (1 assembly per core; 16 in parallel).

itero across MPI nodes

You run the MPI version using a command similar to:

mpirun -hostfile hostfile -n 96 itero assemble mpi --config ndna-test.conf \
    --output mpi \
    --local-cores 16 \
    --iterations 6

If each of your nodes has 16 cores, this will first use 16 cores for the needed bwa alignments of reads to seeds. The code will then distribute locus-specific assemblies across all 96 cores in your cluster (1 assembly per core; 96 in parallel).