---
name: "centrifuge-build"
section: "1"
platform: "linux"
package: "centrifuge"
version: "1.0.4.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/centrifuge-build"
---

# centrifuge-build(1)

building index on all complete bacterial and viral genomes

## NAME

centrifuge-build - building index on all complete bacterial and viral genomes

## SYNOPSIS

**centrifuge-build** \[*options*\]*\* --conversion-table \<table file\> --taxonomy-tree \<taxonomy tree file\> \<reference\_in\> \<cf\_index\_base\>*

## DESCRIPTION

Centrifuge version 1.0.3-beta by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)

- reference\_in

  comma-separated list of files with ref sequences

- centrifuge\_index\_base

  write cf data to files with this dir/basename

## OPTIONS

- **-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

- **-a**/--noauto

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

- **--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.bt2 (packed reference) portion

- **-3**/--justref

  just build .3/.4.bt2 (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)

- **--conversion-table** \<file name\>

  a table that converts any id to a taxonomy id

- **--taxonomy-tree**

  \<file name\>  taxonomy tree

- **--name-table**

  \<file name\>  names corresponding to taxonomic IDs

- **--size-table**

  \<file name\>  table of contig (or genome) sizes

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

  seed for random number generator

- **-q**/--quiet

  verbose output (for debugging)

- **-p**/--threads \<int\>

  number of alignment threads to launch (1)

- **--kmer-count** \<int\>

  k size for counting the number of distinct k-mer

- **-h**/--help

  print detailed description of tool and its options

- **--usage**

  print this usage message

- **--version**

  print version information and quit

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.