diff --git a/NAMESPACE b/NAMESPACE
index 9866790..89d99d8 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ export(appmamba)
 export(appmamba_rc)
 export(arg)
 export(arg0)
+export(bowtie2)
 export(bcftools)
 export(cellranger)
 export(cmd_background)
diff --git a/NEWS.md b/NEWS.md
index 25ee44b..5adf5f3 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,16 @@
 
 * Rename `cmd_conda` to `cmd_codnaenv()`.
 
+* new command `fastp`
+
+* new command `varscan`
+
+* new command `bcftools`
+
+* new command `snpEff`
+
+* new command `bowtie2`
+
 # blit 0.2.0
 
 ## New features
diff --git a/R/cmd-bowtie2.R b/R/cmd-bowtie2.R
new file mode 100644
index 0000000..9e3c592
--- /dev/null
+++ b/R/cmd-bowtie2.R
@@ -0,0 +1,63 @@
+#' Run bowtie2
+#'
+#' Bowtie 2 is an ultrafast and memory-efficient tool 
+#' for aligning sequencing reads to long reference sequences. 
+#' It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, 
+#' and particularly good at aligning to relatively long (e.g. mammalian) genomes. 
+#' Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: 
+#' for the human genome, its memory footprint is typically around 3.2 GB. 
+#' Bowtie 2 supports gapped, local, and paired-end alignment modes.
+#' 
+#' @param index Path to bowtie2 index prefix (without file extensions).
+#' @param reads A character vector of FASTQ files used as input to bowtie2.
+#' @param ofile A string of path to the output sam file.
+#' @param ... `r rd_dots("bowtie2")`.
+#' @param bowtie2 `r rd_cmd("bowtie2")`.
+#' @family command
+#' @inherit exec return
+#' @seealso
+#' - <https://bowtie-bio.sourceforge.net/bowtie2/index.shtml>
+#'
+#' `r rd_seealso()`
+#' @export
+bowtie2 <- make_command(
+  "bowtie2",
+  function(
+    index,
+    reads,
+    ofile,
+    ...,
+    bowtie2 = NULL
+  ){
+    assert_string(bowtie2, allow_empty = FALSE, allow_null = TRUE)
+    Bowtie2$new(
+      cmd = bowtie2,
+      ...,
+      index = index,
+      reads = reads,
+      ofile = ofile
+    )
+  }
+)
+
+Bowtie2 <- R6Class(
+  "Bowtie2",
+  inherit = Command,
+  private = list(
+    alias = function() "bowtie2",
+    setup_help_params = function() "--help",
+    setup_command_params = function(index, reads, ofile){
+      c(
+        arg0("-x", index),
+        if (length(reads) == 1L){
+          arg0("-U", reads)
+        } else if (length(reads) == 2L){
+          arg0("-1", reads[1], "-2", reads[2])
+        } else {
+          cli::cli_abort("{.arg reads} must be of length 1 or 2")
+        },
+        arg0("-S", ofile)
+      )
+    }
+  )
+)
diff --git a/man/allele_counter.Rd b/man/allele_counter.Rd
index 7ad66ff..e426fff 100644
--- a/man/allele_counter.Rd
+++ b/man/allele_counter.Rd
@@ -43,6 +43,7 @@ between some other projects, specifically \code{AscatNGS} and \code{Battenberg}.
 }
 
 Other \code{commands}:
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/bowtie2.Rd b/man/bowtie2.Rd
new file mode 100644
index 0000000..6d0563b
--- /dev/null
+++ b/man/bowtie2.Rd
@@ -0,0 +1,57 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cmd-bowtie2.R
+\name{bowtie2}
+\alias{bowtie2}
+\title{Run bowtie2}
+\usage{
+bowtie2(index, reads, ofile, ..., bowtie2 = NULL)
+}
+\arguments{
+\item{index}{Path to bowtie2 index prefix (without file extensions).}
+
+\item{reads}{A character vector of FASTQ files used as input to bowtie2.}
+
+\item{ofile}{A string of path to the output sam file.}
+
+\item{...}{<\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \code{bowtie2} 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(bowtie2())}.}
+
+\item{bowtie2}{A string of path to \code{bowtie2} command.}
+}
+\value{
+A \code{command} object.
+}
+\description{
+Bowtie 2 is an ultrafast and memory-efficient tool
+for aligning sequencing reads to long reference sequences.
+It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters,
+and particularly good at aligning to relatively long (e.g. mammalian) genomes.
+Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small:
+for the human genome, its memory footprint is typically around 3.2 GB.
+Bowtie 2 supports gapped, local, and paired-end alignment modes.
+}
+\seealso{
+\itemize{
+\item \url{https://bowtie-bio.sourceforge.net/bowtie2/index.shtml}
+\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{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{trust4}()}
+}
+\concept{command}
diff --git a/man/cellranger.Rd b/man/cellranger.Rd
index 3d58a79..6123025 100644
--- a/man/cellranger.Rd
+++ b/man/cellranger.Rd
@@ -48,6 +48,7 @@ cellranger(
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/conda.Rd b/man/conda.Rd
index a77cd79..b4f24af 100644
--- a/man/conda.Rd
+++ b/man/conda.Rd
@@ -29,6 +29,7 @@ Run conda
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{fastp}()},
diff --git a/man/exec.Rd b/man/exec.Rd
index 24363a5..d8ed305 100644
--- a/man/exec.Rd
+++ b/man/exec.Rd
@@ -21,6 +21,7 @@ Invoke a System Command
 
 \itemize{
 \item \code{\link[=allele_counter]{allele_counter()}}
+\item \code{\link[=bowtie2]{bowtie2()}}
 \item \code{\link[=bcftools]{bcftools()}}
 \item \code{\link[=cellranger]{cellranger()}}
 \item \code{\link[=conda]{conda()}}
diff --git a/man/fastp.Rd b/man/fastp.Rd
index fe62c54..d6ca9a8 100644
--- a/man/fastp.Rd
+++ b/man/fastp.Rd
@@ -33,6 +33,7 @@ and quality control for FastQ data.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/fastq_pair.Rd b/man/fastq_pair.Rd
index a424b25..e14e171 100644
--- a/man/fastq_pair.Rd
+++ b/man/fastq_pair.Rd
@@ -54,6 +54,7 @@ they demand paired end files have the same number of reads.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/gistic2.Rd b/man/gistic2.Rd
index 6b919ef..fd616ba 100644
--- a/man/gistic2.Rd
+++ b/man/gistic2.Rd
@@ -51,6 +51,7 @@ deletion, and it lists genes found in each "wide peak" region.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/kraken2.Rd b/man/kraken2.Rd
index 13f460c..e4e2a4b 100644
--- a/man/kraken2.Rd
+++ b/man/kraken2.Rd
@@ -57,6 +57,7 @@ given k-mer.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/kraken_tools.Rd b/man/kraken_tools.Rd
index a0f820f..43aafc3 100644
--- a/man/kraken_tools.Rd
+++ b/man/kraken_tools.Rd
@@ -33,6 +33,7 @@ analysis of Kraken results.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/perl.Rd b/man/perl.Rd
index 48c2918..c801407 100644
--- a/man/perl.Rd
+++ b/man/perl.Rd
@@ -30,6 +30,7 @@ years of development.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/pyscenic.Rd b/man/pyscenic.Rd
index 4a815b4..ba7141c 100644
--- a/man/pyscenic.Rd
+++ b/man/pyscenic.Rd
@@ -30,6 +30,7 @@ Run pyscenic
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/python.Rd b/man/python.Rd
index 5470219..5744f93 100644
--- a/man/python.Rd
+++ b/man/python.Rd
@@ -30,6 +30,7 @@ systems more effectively.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/samtools.Rd b/man/samtools.Rd
index b2af24c..2f4bef6 100644
--- a/man/samtools.Rd
+++ b/man/samtools.Rd
@@ -32,6 +32,7 @@ systems more effectively.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/seqkit.Rd b/man/seqkit.Rd
index c753423..5c9d737 100644
--- a/man/seqkit.Rd
+++ b/man/seqkit.Rd
@@ -30,6 +30,7 @@ Run seqkit
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/trust4.Rd b/man/trust4.Rd
index a40463c..4603269 100644
--- a/man/trust4.Rd
+++ b/man/trust4.Rd
@@ -85,6 +85,7 @@ data
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},