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:

• k{kmer_size}.contigs.fa contains the contigs assembled in the round of kmer_size, they can be converted to a SPAdes-like FASTG file for visualiztion
• k{kmer_size}.addi.fa contains the contigs assembled after iteratively removing local low coverage unitigs in the round of kmer_size
• k{kmer_size}.local.fa contains the locally assembled contigs in the round of kmer_size
• k{kmer_size}.final.contigs.fa contains the stand-alone contigs in the round of kmer_size; if local assembly is turned on, the file will be empty