MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. See the MEGAHIT home page for more info.
MEGAHIT can be run by the following command. As our compute instance have multiple cores, we use the option -t 14 to tell MEGAHIT it should use 14 parallel threads. The output will be redirected to file `megahit.log`:
cd /vol/spool/workdir/assembly/
qsub -cwd -pe multislot 14 -N megahit -b y \
/usr/bin/megahit -1 read1.fq -2 read2.fq -t 14 -o megahit_outThe contig sequences are located in the megahit_out directory in file final.contigs.fa. Again, let's get some basic statistics on the contigs:
getN50.pl -s 500 -f megahit_out/final.contigs.fa