CENTRIFUGE

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.