darwin-gpu¶

Description¶

A GPU implementation of Darwin, a hardware-friendly DNA aligner. It consists of two parts: D-SOFT and GACT, which represent typical seed-and-extend methods. D-SOFT (Diagonal-band based Seed Overlapping based Filtration Technique) filters the search space by counting non-overlapping bases in matching Kmers in a band of diagonals. GACT (Genomic Alignment using Constant Tracebackmemory) can align reads of arbitrary length using constant memory for the compute-intensive step.

Environment Modules¶

Run module spider darwin-gpu to find out what environment modules are available for this application.

Environment Variables¶

HPC_DARWINGPU_DIR - installation directory

Additional Usage Information¶

Application must be run from a copy of the installation directory because dependencies are hard-coded to be relative the compiled binary (darwin).

$ cp -r $HPC_DARWINGPU_DIR /blue/$GROUP/$USER/mydarwin-gpu
$ cd /blue/$GROUP/$USER/mydarwin-gpu
$ darwin -h

Usage: ./reference_guided <REFERENCE>.fasta <READS>.fasta [NUM_BLOCKS THREADS_PER_BLOCK]

Categories¶

genomics, alignment