MASH based taxonomic assignment for genomic assemblies or read sets

SPARSE allows ultra-efficient taxonomic assignment with genomic assemblies or read sets, by using MASH to approximate average nucleotide identities (ANI).

genomic assembly (fasta format):

sparse mash --dbname refseq --query <assembly file>

Read set (in fastq format, either gzipped or not) :

sparse mash --dbname refseq --query <read file> --read