Getting Started • Rminibwa

Rminibwa installs a minibwa executable built from its vendored upstream source, plus native R bindings for index-backed mapping.

library(Rminibwa)
minibwa_available()

Check the packaged executable:

minibwa_path()
minibwa_version()

Index a reference and map reads:

prefix <- minibwa_index("ref.fa", threads = 8)
aln <- minibwa_map(prefix, "reads.fq.gz", format = "paf", threads = 8)

Write SAM or PAF output directly to a file by setting output:

minibwa_map(prefix, c("read1.fq.gz", "read2.fq.gz"), output = "aln.sam")

The CLI layer is intentionally thin and stays close to upstream behavior. The native batch API is the preferred hot path for in-process R workflows.