---
name: "bowtie2-build"
section: "1"
platform: "linux"
package: "bowtie2"
version: "2.5.4-1+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bowtie2-build"
---

# bowtie2-build(1)

wrapper for bowtie2-build-\*

## NAME

bowtie2-build - wrapper for bowtie2-build-\*

## SYNOPSIS

**bowtie2-build** \[*options*\]*\* \<reference\_in\> \<bt2\_index\_base\>*

## DESCRIPTION

- Bowtie 2 version 2.5.4 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)

  - reference\_in

  comma-separated list of files with ref sequences

- bt2\_index\_base

  write bt2 data to files with this dir/basename

\*\*\* Bowtie 2 indexes will work with Bowtie v1.2.3 and later. \*\*\*

## OPTIONS

**-f** reference files are Fasta (default)

- **-c**

  reference sequences given on cmd line (as \<reference\_in\>)

- **--large-index**

  force generated index to be 'large', even if ref has fewer than 4 billion nucleotides

- **--debug**

  use the debug binary; slower, assertions enabled

- **--verbose**

  log the issued command

- **-a**/--noauto

  disable automatic **-p**/--bmax/--dcv memory-fitting

- **-p**/--packed

  use packed strings internally; slower, less memory

- **--bmax** \<int\>

  max bucket sz for blockwise suffix-array builder

- **--bmaxdivn** \<int\>

  max bucket sz as divisor of ref len (default: 4)

- **--dcv** \<int\>

  diff-cover period for blockwise (default: 1024)

- **--nodc**

  disable diff-cover (algorithm becomes quadratic)

- **-r**/--noref

  don't build .3/.4 index files

- **-3**/--justref

  just build .3/.4 index files

- **-o**/--offrate \<int\>

  SA is sampled every 2^\<int\> BWT chars (default: 5)

- **-t**/--ftabchars \<int\>

  \# of chars consumed in initial lookup (default: 10)

- **--threads** \<int\>

  \# of threads

- **--seed** \<int\>

  seed for random number generator

- **-q**/--quiet

  verbose output (for debugging)

- **--h**/--help

  print this message and quit

- **--version**

  print version information and quit