MEGAHIT Assembly
================

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 <https://github.com/voutcn/megahit/>`_ 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 /mnt/WGS-data

  megahit -1 read1.fq -2 read2.fq -t 28 -o megahit_out

The 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