centrifuge1

Rapid and memory-efficient system for classification of dna sequences

Overview

Centrifuge version 1.0.3-beta by the Centrifuge developer team ([email protected]) 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

History

Debian 13 (Trixie) to Debian 12 (Bookworm): the text shown here
Debian 11 (Bullseye) to Debian 10 (Buster)

--al since Debian 12 (Bookworm); --al-conc since Debian 12 (Bookworm); --ignore-quals since Debian 12 (Bookworm); --int-quals since Debian 12 (Bookworm); --min-hitlen since Debian 12 (Bookworm); --min-totallen since Debian 12 (Bookworm); --mm since Debian 12 (Bookworm); --nofw since Debian 12 (Bookworm); --norc since Debian 12 (Bookworm); --out-fmt since Debian 12 (Bookworm); --phred33 since Debian 12 (Bookworm); --phred64 since Debian 12 (Bookworm); --qc-filter since Debian 12 (Bookworm); --qseq since Debian 12 (Bookworm); --seed since Debian 12 (Bookworm); --tab-fmt-cols since Debian 12 (Bookworm); --un since Debian 12 (Bookworm); --un-conc since Debian 12 (Bookworm); --version since Debian 12 (Bookworm); -c since Debian 12 (Bookworm); -f since Debian 12 (Bookworm); -q since Debian 12 (Bookworm); -r since Debian 12 (Bookworm).