---
name: "bowtie-build"
section: "1"
platform: "linux"
package: "bowtie"
version: "1.3.1-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bowtie-build"
---

# bowtie-build(1)

building a colorspace index for bowtie

## NAME

bowtie-build - building a colorspace index for bowtie

## SYNOPSIS

**bowtie-build** \[*options*\]*\* \<reference\_in\> \<ebwt\_outfile\_base\>*

## DESCRIPTION

- reference\_in

  comma-separated list of files with ref sequences

- ebwt\_outfile\_base

  write Ebwt data to files with this dir/basename

## OPTIONS

- **-f**

  reference files are Fasta (default)

- **-c**

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

- **--large-index**

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

- **-a**/--noauto

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

- **-p**/--packed

  use packed strings internally; slower, uses less mem

- **--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.ebwt (packed reference) portion

- **-3**/--justref

  just build .3/.4.ebwt (packed reference) portion

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

  SA is sampled every 2^offRate BWT chars (default: 5)

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

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

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

  \# of threads

- **--ntoa**

  convert Ns in reference to As

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

  seed for random number generator

- **-q**/--quiet

  verbose output (for debugging)

- **-h**/--help

  print detailed description of tool and its options

- **--usage**

  print this usage message

- **--version**

  print version information and quit

64-bit Built on Debian-reproducible Thu, 25 Jan 2024 12:27:31 +0100 Compiler: gcc version 13.2.0 Options: **-O3** **-Wl**,--hash-style=both **-DPOPCNT\_CAPABILITY** **-Wdate-time** **-D\_FORTIFY\_SOURCE**=*2* **-g** **-O2** **-ffile-prefix-map=**.=. **-fstack-protector-strong** **-fstack-clash-protection** **-Wformat** **-Werror**=*format-security* **-fcf-protection**  **-g** **-O2** **-ffile-prefix-map=**.=. **-fstack-protector-strong** **-fstack-clash-protection** **-Wformat** **-Werror**=*format-security* **-fcf-protection** **-std**=*c*++03 **-Wl**,-z,relro **-Wl**,-z,now Sizeof {int, long, long long, void\*, size\_t, off\_t}: {4, 8, 8, 8, 8, 8}