diff --git a/NAMESPACE b/NAMESPACE
index 8913399..d72f6da 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,6 +10,7 @@ export(arg0)
 export(bcftools)
 export(bedtools)
 export(bowtie2)
+export(bwa)
 export(cellranger)
 export(cmd_background)
 export(cmd_conda)
diff --git a/R/cmd-bwa.R b/R/cmd-bwa.R
new file mode 100644
index 0000000..d83b343
--- /dev/null
+++ b/R/cmd-bwa.R
@@ -0,0 +1,48 @@
+#' Run BWA
+#'
+#' BWA is a software package that aligns low-divergence sequences to a
+#' large reference genome, such as the human genome
+#' @param subcmd Sub-Command of BWA (e.g., "index", "mem").
+#' @param ... `r rd_dots("bwa")`.
+#' @param bwa `r rd_cmd("bwa")`.
+#' @inherit exec return
+#' @seealso
+#' - <http://bio-bwa.sourceforge.net/>
+#'
+#' `r rd_seealso()`
+#' @examples
+#' \dontrun{
+#' # Index reference genome
+#' bwa("index", "-a", "bwtsw", "reference.fa") |>
+#'   cmd_run()
+#'
+#' # Paired-end sequence alignment
+#' bwa("mem", "-t", "4", "reference.fa", "read1.fq", "read2.fq") |>
+#'   cmd_run(stdout = "output.sam")
+#'
+#' # Single-end alignment (generate sai file)
+#' bwa("aln", "-t", "4", "reference.fa", "read.fq") |>
+#'   cmd_run(stdout = "read.sai")
+#' }
+#' @family command
+#' @export
+bwa <- make_command(
+  "bwa",
+  function(subcmd = NULL, ..., bwa = NULL) {
+    assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
+    assert_string(bwa, allow_empty = FALSE, allow_null = TRUE)
+    BWA$new(cmd = bwa, ..., subcmd = subcmd)
+  }
+)
+
+BWA <- R6Class(
+  "BWA",
+  inherit = Command,
+  private = list(
+    alias = function() "bwa",
+    setup_help_params = function() "--help",
+    combine_params = function(subcmd) {
+      c(subcmd, super$combine_params())
+    }
+  )
+)
diff --git a/blit.Rproj b/blit.Rproj
index aaa62a5..69fafd4 100644
--- a/blit.Rproj
+++ b/blit.Rproj
@@ -5,8 +5,13 @@ SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
 Encoding: UTF-8
 
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 LineEndingConversion: Posix
diff --git a/man/allele_counter.Rd b/man/allele_counter.Rd
index cfa696b..1d2fa45 100644
--- a/man/allele_counter.Rd
+++ b/man/allele_counter.Rd
@@ -46,6 +46,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/bcftools.Rd b/man/bcftools.Rd
index f884a5e..fd249fb 100644
--- a/man/bcftools.Rd
+++ b/man/bcftools.Rd
@@ -36,6 +36,7 @@ Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/bedtools.Rd b/man/bedtools.Rd
index 869b61c..e85eb08 100644
--- a/man/bedtools.Rd
+++ b/man/bedtools.Rd
@@ -33,6 +33,7 @@ Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/bowtie2.Rd b/man/bowtie2.Rd
index 361c175..a103f2d 100644
--- a/man/bowtie2.Rd
+++ b/man/bowtie2.Rd
@@ -42,6 +42,7 @@ Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/bwa.Rd b/man/bwa.Rd
new file mode 100644
index 0000000..908161b
--- /dev/null
+++ b/man/bwa.Rd
@@ -0,0 +1,68 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cmd-bwa.R
+\name{bwa}
+\alias{bwa}
+\title{Run BWA}
+\usage{
+bwa(subcmd = NULL, ..., bwa = NULL)
+}
+\arguments{
+\item{subcmd}{Sub-Command of BWA (e.g., "index", "mem").}
+
+\item{...}{<\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \code{bwa} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \code{cmd_help(bwa())}.}
+
+\item{bwa}{A string of path to \code{bwa} command.}
+}
+\value{
+A \code{command} object.
+}
+\description{
+BWA is a software package that aligns low-divergence sequences to a
+large reference genome, such as the human genome
+}
+\examples{
+\dontrun{
+# Index reference genome
+bwa("index", "-a", "bwtsw", "reference.fa") |>
+  cmd_run()
+
+# Paired-end sequence alignment
+bwa("mem", "-t", "4", "reference.fa", "read1.fq", "read2.fq") |>
+  cmd_run(stdout = "output.sam")
+
+# Single-end alignment (generate sai file)
+bwa("aln", "-t", "4", "reference.fa", "read.fq") |>
+  cmd_run(stdout = "read.sai")
+}
+}
+\seealso{
+\itemize{
+\item \url{http://bio-bwa.sourceforge.net/}
+\item \code{\link[=cmd_wd]{cmd_wd()}}/\code{\link[=cmd_envvar]{cmd_envvar()}}/\code{\link[=cmd_envpath]{cmd_envpath()}}/\code{\link[=cmd_condaenv]{cmd_condaenv()}}
+\item \code{\link[=cmd_on_start]{cmd_on_start()}}/\code{\link[=cmd_on_exit]{cmd_on_exit()}}
+\item \code{\link[=cmd_on_succeed]{cmd_on_succeed()}}/\code{\link[=cmd_on_fail]{cmd_on_fail()}}
+\item \code{\link[=cmd_parallel]{cmd_parallel()}}
+}
+
+Other \code{commands}:
+\code{\link{allele_counter}()},
+\code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
+\code{\link{cellranger}()},
+\code{\link{conda}()},
+\code{\link{fastp}()},
+\code{\link{fastq_pair}()},
+\code{\link{gistic2}()},
+\code{\link{kraken2}()},
+\code{\link{kraken_tools}()},
+\code{\link{perl}()},
+\code{\link{pyscenic}()},
+\code{\link{python}()},
+\code{\link{samtools}()},
+\code{\link{seqkit}()},
+\code{\link{snpEff}()},
+\code{\link{trust4}()},
+\code{\link{varscan}()}
+}
+\concept{command}
diff --git a/man/cellranger.Rd b/man/cellranger.Rd
index f52c025..8b51c7e 100644
--- a/man/cellranger.Rd
+++ b/man/cellranger.Rd
@@ -51,6 +51,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
 \code{\link{fastq_pair}()},
diff --git a/man/conda.Rd b/man/conda.Rd
index 9fe0555..6ca35db 100644
--- a/man/conda.Rd
+++ b/man/conda.Rd
@@ -32,6 +32,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{fastp}()},
 \code{\link{fastq_pair}()},
diff --git a/man/exec.Rd b/man/exec.Rd
index 31fb607..32bc558 100644
--- a/man/exec.Rd
+++ b/man/exec.Rd
@@ -24,6 +24,7 @@ Invoke a System Command
 \item \code{\link[=bcftools]{bcftools()}}
 \item \code{\link[=bedtools]{bedtools()}}
 \item \code{\link[=bowtie2]{bowtie2()}}
+\item \code{\link[=bwa]{bwa()}}
 \item \code{\link[=cellranger]{cellranger()}}
 \item \code{\link[=conda]{conda()}}
 \item \code{\link[=fastp]{fastp()}}
diff --git a/man/fastp.Rd b/man/fastp.Rd
index ec3e879..4546142 100644
--- a/man/fastp.Rd
+++ b/man/fastp.Rd
@@ -36,6 +36,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastq_pair}()},
diff --git a/man/fastq_pair.Rd b/man/fastq_pair.Rd
index 3764bc6..ebd9fbf 100644
--- a/man/fastq_pair.Rd
+++ b/man/fastq_pair.Rd
@@ -57,6 +57,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/gistic2.Rd b/man/gistic2.Rd
index 42e9a6a..a1f8c0f 100644
--- a/man/gistic2.Rd
+++ b/man/gistic2.Rd
@@ -54,6 +54,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/kraken2.Rd b/man/kraken2.Rd
index 0a1adc0..c67271a 100644
--- a/man/kraken2.Rd
+++ b/man/kraken2.Rd
@@ -60,6 +60,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/kraken_tools.Rd b/man/kraken_tools.Rd
index fece02b..813ad80 100644
--- a/man/kraken_tools.Rd
+++ b/man/kraken_tools.Rd
@@ -36,6 +36,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/perl.Rd b/man/perl.Rd
index c2b8c8e..0b5d27a 100644
--- a/man/perl.Rd
+++ b/man/perl.Rd
@@ -33,6 +33,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/pyscenic.Rd b/man/pyscenic.Rd
index 63f20fc..5fa2b6a 100644
--- a/man/pyscenic.Rd
+++ b/man/pyscenic.Rd
@@ -33,6 +33,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/python.Rd b/man/python.Rd
index d4e32a3..b733052 100644
--- a/man/python.Rd
+++ b/man/python.Rd
@@ -33,6 +33,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/samtools.Rd b/man/samtools.Rd
index 5b1c133..7a3d4a5 100644
--- a/man/samtools.Rd
+++ b/man/samtools.Rd
@@ -35,6 +35,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/seqkit.Rd b/man/seqkit.Rd
index fcfe722..5dff545 100644
--- a/man/seqkit.Rd
+++ b/man/seqkit.Rd
@@ -33,6 +33,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/snpEff.Rd b/man/snpEff.Rd
index 79b611a..c6fa9a1 100644
--- a/man/snpEff.Rd
+++ b/man/snpEff.Rd
@@ -35,6 +35,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/trust4.Rd b/man/trust4.Rd
index cdcc7bd..3956a32 100644
--- a/man/trust4.Rd
+++ b/man/trust4.Rd
@@ -88,6 +88,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/varscan.Rd b/man/varscan.Rd
index 03ae011..6c949eb 100644
--- a/man/varscan.Rd
+++ b/man/varscan.Rd
@@ -35,6 +35,7 @@ Other \code{commands}:
 \code{\link{bcftools}()},
 \code{\link{bedtools}()},
 \code{\link{bowtie2}()},
+\code{\link{bwa}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/tests/testthat/test-exec.R b/tests/testthat/test-exec.R
index 2e848cc..e325bef 100644
--- a/tests/testthat/test-exec.R
+++ b/tests/testthat/test-exec.R
@@ -8,6 +8,13 @@ testthat::test_that("`bedtools()` works as expected", {
     bedtools() |> cmd_help()
 })
 
+testthat::test_that("`bwa()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("bwa")))
+  bwa() |> cmd_help()
+  bwa("index") |> cmd_help()
+  bwa("mem") |> cmd_help()
+})
+
 testthat::test_that("`cellranger()` works as expected", {
     testthat::skip_if_not(nzchar(Sys.which("cellranger")))
     cellranger() |> cmd_help()
@@ -96,4 +103,30 @@ testthat::test_that("`bcftools()` works as expected", {
 testthat::test_that("`bowtie2()` works as expected", {
   testthat::skip_if_not(nzchar(Sys.which("bowtie2")))
   bowtie2() |> cmd_help()
-})
\ No newline at end of file
+})
+
+testthat::test_that("`varscan()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("varscan")))
+  varscan() |> cmd_help()
+})
+
+testthat::test_that("`fastp()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("fastp")))
+  fastp() |> cmd_help()
+})
+
+
+testthat::test_that("`snpeff()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("snpeff")))
+  snpeff() |> cmd_help()
+})
+
+testthat::test_that("`bcftools()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("bcftools")))
+  bcftools() |> cmd_help()
+})
+
+testthat::test_that("`bowtie2()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("bowtie2")))
+  bowtie2() |> cmd_help()
+})