MEGAHIT toolkit's contig2fastg

Contig2fastg is a subprogram within the MEGAHIT toolkit. It converts MEGAHIT's contigs (.fa) to assembly graphs (.fastg) that can be utilized for protein/peptide identification via graph2pro and can also be visualized via Bandage.

EXAMPLE

Command:

megahit_toolkit contig2fastg 99 intermediate_contigs/k99.contigs.fa > k99.contigs.fastg

k99.contigs.fa

>k21_1 flag=3 multi=1.0486 len=576

CGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTC...

k99.contigs.fastg

>NODE_1_length_576_cov_1.0486_ID_1:NODE_1_length_576_cov_1.0486_ID_1;

CGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTC...

MEGAHIT

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. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5.

Project links:

MEGAHIT and MEGAHIT Toolkit: https://github.com/voutcn/megahit

Graph2Pro-Var: https://github.com/COL-IU/graph2pro-var

Bandage: http://rrwick.github.io/Bandage/