contigs output by MEGAHIT

The FASTA file final.contigs.fa (or OUTPUT_PREFIX.contigs.fa if --out-prefix is specified) is the final result of the assembly.

For files in the folder intermediate_contigs:

• kK.contigs.fa contains the contigs assembled from the de Bruijn graph of order-K, they can be converted to a SPAdes-like FASTG file for visualization
• kK.addi.fa contains the contigs assembled after iteratively removing local low coverage unitigs in the de Bruijn graph of order-K
• kK.local.fa contains the locally assembled contigs for k=K
• kK.final.contigs.fa contains the stand-alone contigs for k=K; if local assembly is turned on, the file will be empty