Dockerfile for BWA-MEM2 (for mapping DNA sequences against a large reference genome) and SAMtools (for interacting with high-thouroughput sequencing data) used for pipeline-align-DNA.
The current BWA-MEM2 image with SAMtools is located in UCLAHS-CDS GitHub Packages: https://github.com/orgs/uclahs-cds/packages/container/package/bwa-mem2.
Documentation for BWA-MEM2 can be found here: https://github.com/bwa-mem2/bwa-mem2. Documentation for SAMtools: http://www.htslib.org/doc/.
| Tool | Version |
|---|---|
| BWA-MEM2 | 2.2.1 |
| SAMtools | 1.17 |
-
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H, Twelve years of SAMtools and BCFtools, GigaScience (2021) 10(2) giab008
-
Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019.