| name | bwa-mem2 |
| description | Architecture-aware faster BWA-MEM for Illumina reads to contigs/genomes. Use when a BWA-MEM workflow is required but throughput must improve, or when migrating from classic bwa mem. Upstream: https://github.com/bwa-mem2/bwa-mem2. Index format is NOT compatible with classic bwa index.
|
| license | MIT |
| category | analysis-tools |
| tags | ["mapping","alignment","short-read","bwa"] |
| upstream | https://github.com/bwa-mem2/bwa-mem2 |
| stage | mapping |
BWA-MEM2
Upstream: bwa-mem2/bwa-mem2
Citation
Vasimuddin, M., Misra, S., Li, H. & Aluru, S. Efficient architecture-aware
acceleration of BWA-MEM for multicore systems. IEEE IPDPS 314–324 (2019).
https://doi.org/10.1109/IPDPS.2019.00041
Classic algorithm context: Li, H. Aligning sequence reads, clone sequences and
assembly contigs with BWA-MEM. arXiv (2013).
https://doi.org/10.48550/arXiv.1303.3997
Analytical thinking
BWA-MEM2 keeps the MEM mapping model familiar to BWA users while speeding
alignment on modern CPUs. Critical pitfall: bwa-mem2 index ≠ bwa index —
never point bwa-mem2 mem at a classic BWA index (or the reverse).
For new metagenome coverage projects, strobealign or bowtie2 may be simpler;
choose BWA-MEM2 when SOPs/scripts already assume BWA-MEM flags and SAM fields.
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| Index | From bwa-mem2 index | Rebuild if upgrading major version |
| RAM | Index ~ reference size class | Large co-assemblies need big nodes |
How to run
conda install -c bioconda bwa-mem2 samtools
bwa-mem2 index contigs.fa
bwa-mem2 mem -t 16 contigs.fa \
temp/hr/${id}_1.fastq temp/hr/${id}_2.fastq \
2> temp/map/${id}.bwa-mem2.log \
| samtools sort -@ 8 -o temp/map/${id}.bam
samtools index temp/map/${id}.bam
Key parameters
| Option | Guidance |
|---|
-t | Threads |
-R | Read group (@RG) when merging multi-lane BAMs |
-K | Process chunk size; raise on huge inputs if supported |
Decision tree
Need BWA-MEM-like mapping?
├─ Legacy classic bwa only available → bwa
├─ Speed on modern CPUs → bwa-mem2
└─ Greenfield metagenome coverage → strobealign or bowtie2
Troubleshooting
| Symptom | Action |
|---|
| Index load errors | Rebuild with bwa-mem2 index |
| Divergent SM tags | Set -R consistently across lanes |
| Huge unsorted SAM | Stream to samtools sort (never dump SAM) |
Related skills
bwa · bowtie2 · strobealign · samtools · coverm · metabat2
