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.
There is one application service specification defined here:
- MetagenomicReadMapping: Service that that provides the backend for the BV-BRC web inerface; it takes reads as input.
The code in this module provides the BV-BRC application service wrapper scripts for the Metagenomic Read Mapping service as well as some backend utilities:
| Script name | Purpose |
|---|---|
| App-MetagenomicReadMapping.pl | App script for the metagenomic read mapping service |
Clausen, P.T., F.M. Aarestrup, and O. Lund, Rapid and precise alignment of raw reads against redundant databases with KMA. BMC bioinformatics, 2018. 19(1): p. 307.
Alcock, B.P., et al., CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic acids research, 2020. 48(D1): p. D517-D525.
Liu, B., et al., VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic acids research, 2019. 47(D1): p. D687-D692.
Kent, W.J., BLAT—the BLAST-like alignment tool. Genome research, 2002. 12(4): p. 656-664.