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

# centrifuge(1)

rapid and memory-efficient system for classification of DNA sequences

## NAME

centrifuge - rapid and memory-efficient system for classification of DNA sequences

## DESCRIPTION

Centrifuge version 1.0.3-beta by the Centrifuge developer team (centrifuge.metagenomics@gmail.com) Usage:

-

  centrifuge \[options\]\* **-x** \<cf-idx\> {-1 \<m1\> **-2** \<m2\> \| **-U** \<r\>} \[-S \<filename\>\] \[--report-file \<report\>\]

- \<cf-idx\>

  Index filename prefix (minus trailing .X.cf).

- \<m1\>

  Files with #1 mates, paired with files in \<m2\>. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).

- \<m2\>

  Files with #2 mates, paired with files in \<m1\>. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).

- \<r\>

  Files with unpaired reads. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).

- \<filename\>

  File for classification output (default: stdout)

- \<report\>

  File for tabular report output (default: centrifuge\_report.tsv)

-

  \<m1\>, \<m2\>, \<r\> can be comma-separated lists (no whitespace) and can be specified many times.  E.g. '-U file1.fq,file2.fq **-U** file3.fq'.

Options (defaults in parentheses):

-

  Input:

- **-q**

  query input files are FASTQ .fq/.fastq (default)

- **--qseq**

  query input files are in Illumina's qseq format

- **-f**

  query input files are (multi-)FASTA .fa/.mfa

- **-r**

  query input files are raw one-sequence-per-line

- **-c**

  \<m1\>, \<m2\>, \<r\> are sequences themselves, not files

- **-s**/--skip \<int\>

  skip the first \<int\> reads/pairs in the input (none)

- **-u**/--upto \<int\>

  stop after first \<int\> reads/pairs (no limit)

- **-5**/--trim5 \<int\>

  trim \<int\> bases from 5'/left end of reads (0)

- **-3**/--trim3 \<int\>

  trim \<int\> bases from 3'/right end of reads (0)

- **--phred33**

  qualities are Phred+33 (default)

- **--phred64**

  qualities are Phred+64

- **--int-quals**

  qualities encoded as space-delimited integers

- **--ignore-quals**

  treat all quality values as 30 on Phred scale (off)

- **--nofw**

  do not align forward (original) version of read (off)

- **--norc**

  do not align reverse-complement version of read (off)

### Classification:

- **--min-hitlen** \<int\>

  minimum length of partial hits (default 22, must be greater than 15)

- **--min-totallen** \<int\>

  minimum summed length of partial hits per read (default 0)

**--host-taxids** \<taxids\> comma-separated list of taxonomic IDs that will be preferred in classification

**--exclude-taxids** \<taxids\> comma-separated list of taxonomic IDs that will be excluded in classification

-

  Output:

- **--out-fmt** \<str\>

  define output format, either 'tab' or 'sam' (tab)

- **--tab-fmt-cols** \<str\>

  columns in tabular format, comma separated default: readID,seqID,taxID,score,2ndBestScore,hitLength,queryLength,numMatches

- **-t**/--time

  print wall-clock time taken by search phases

- **--un** \<path\>

  write unpaired reads that didn't align to \<path\>

- **--al** \<path\>

  write unpaired reads that aligned at least once to \<path\>

- **--un-conc** \<path\>

  write pairs that didn't align concordantly to \<path\>

- **--al-conc** \<path\>

  write pairs that aligned concordantly at least once to \<path\>

-

  (Note: for **--un**, **--al**, **--un-conc**, or **--al-conc**, add '-gz' to the option name, e.g. **--un-gz** \<path\>, to gzip compress output, or add '-bz2' to bzip2 compress output.) **--quiet**               print nothing to stderr except serious errors **--met-file** \<path\>     send metrics to file at \<path\> (off) **--met-stderr**          send metrics to stderr (off) **--met** \<int\>           report internal counters & metrics every \<int\> secs (1)

-

  Performance:

**-o**/--offrate \<int\> override offrate of index; must be \>= index's offrate

**-p**/--threads \<int\> number of alignment threads to launch (1)

- **--mm**

  use memory-mapped I/O for index; many instances can share

-

  Other:

- **--qc-filter**

  filter out reads that are bad according to QSEQ filter

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

  seed for random number generator (0)

**--non-deterministic** seed rand. gen. arbitrarily instead of using read attributes

- **--version**

  print version information and quit

- **-h**/--help

  print this usage message

## AUTHOR

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