De novo Assembly - Golob-Minot/geneshot GitHub Wiki

To identify microbial genes, geneshot will:

• perform de novo assembly of short reads with MEGAHIT,
• identify protein-coding sequences with Prodigal, and
• deduplicate similar gene sequences using MMseqs2

Various flags include:

• --phred_offset: The PHRED offset used by MEGAHIT, default: 33
• --min_identity: Amino acid identity cutoff used by MMseqs2 to combine similar genes, default: 90
• --min_coverage: Length cutoff used by MMseqs2 to combine similar genes, default: 50