Visualizing MEGAHIT's contig graph

This feature is supported in version 0.3.0 or later.

All intermediate contigs assembled in the iteration of kmer_size=k are moved to the folder intermediate_contigs in the output directory. To visualize contig graph in Bandage, the first step is to convert the fasta file(s) intermediate_contigs/k{kmer_size}.contigs.fa into SPAdes-like FASTG format. The following code shows the translation from k99.contigs.fa into k99.fastg.

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

Then the FASTG file k99.fastg can be loaded into Bandage.

Note that final.contigs.fa in the output directory has filtered out some short contigs, thus we recommend using the contigs intermediate_contigs/k.contigs.fa* for visualiztion.