The Metagenomic Read Mapping Service uses KMA to align reads against antibiotic resistance genes, virulence factors, or other custom sets of genes.
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.
This module provides the following application specfication(s):
- Kent, W. James. "BLAT—the BLAST-like alignment tool." Genome research 12.4 (2002): 656-664.
- Jia, Baofeng, et al. "CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database." Nucleic acids research (2016): gkw1004.
- Liu, Bo, et al. "VFDB 2019: a comparative pathogenomic platform with an interactive web interface." Nucleic acids research 47.D1 (2018): D687-D692.
- Philip T.L.C. Clausen, Frank M. Aarestrup & Ole Lund, "Rapid and precise alignment of raw reads against redundant databases with KMA", BMC Bioinformatics, 2018;19:307.