kma : k-mer mapping of raw reads to a redundant database
Database needs to be indexed to use kma for mapping:
kma index -i templates.fsa.gz -o database/name
kma mapping of paired and unpaired read files:
kma -ipe SRR13957123_*.fastq.gz -o test.output -t_db DB_name
kma -i singleEndReads.fq.gz -ipe pairedEnd_*.fq.gz -o output/name -t_db database/name -1t1