Busco

BUSCO is a suite that attempts to provide a quantitative assessment of the completeness in terms of expected gene content of a genome assembly, transcriptome, or annotated gene set. It outputs a file consisting of complete single copy, complete duplicate, fragmented, or missing counts.

For additional information, see the BUSCO documentation.

ml biocontainers busco
# Genome mode
busco -m genome -i INPUT.nucleotideFile -o OUTPUTNAME -l SpeciesLineage
# Protein mode
busco -m protein -i INPUT.amino_acidsFile -o OUTPUTNAME -l SpeciesLineage
# Transcriptome mode
buscso -m transcriptome -i INPUT.nucleotideFile -o OUTPUTNAME -l SpeciesLineage
# can also have it auto determine lineage with --auto-lineage

Parallel Capabilities: Single core default, multithreading options supported.