.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.1.
.TH CENTRIFUGE "1" "October 2021" "centrifuge 1.0.3" "User Commands"
.SH NAME
centrifuge \- rapid and memory-efficient system for classification of DNA sequences
.SH DESCRIPTION
Centrifuge version 1.0.3\-beta by the Centrifuge developer team (centrifuge.metagenomics@gmail.com)
Usage:
.IP
centrifuge [options]* \fB\-x\fR <cf\-idx> {\-1 <m1> \fB\-2\fR <m2> | \fB\-U\fR <r>} [\-S <filename>] [\-\-report\-file <report>]
.TP
<cf\-idx>
Index filename prefix (minus trailing .X.cf).
.TP
<m1>
Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
.TP
<m2>
Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
.TP
<r>
Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
.TP
<filename>
File for classification output (default: stdout)
.TP
<report>
File for tabular report output (default: centrifuge_report.tsv)
.IP
<m1>, <m2>, <r> can be comma\-separated lists (no whitespace) and can be
specified many times.  E.g. '\-U file1.fq,file2.fq \fB\-U\fR file3.fq'.
.PP
Options (defaults in parentheses):
.IP
Input:
.TP
\fB\-q\fR
query input files are FASTQ .fq/.fastq (default)
.TP
\fB\-\-qseq\fR
query input files are in Illumina's qseq format
.TP
\fB\-f\fR
query input files are (multi\-)FASTA .fa/.mfa
.TP
\fB\-r\fR
query input files are raw one\-sequence\-per\-line
.TP
\fB\-c\fR
<m1>, <m2>, <r> are sequences themselves, not files
.TP
\fB\-s\fR/\-\-skip <int>
skip the first <int> reads/pairs in the input (none)
.TP
\fB\-u\fR/\-\-upto <int>
stop after first <int> reads/pairs (no limit)
.TP
\fB\-5\fR/\-\-trim5 <int>
trim <int> bases from 5'/left end of reads (0)
.TP
\fB\-3\fR/\-\-trim3 <int>
trim <int> bases from 3'/right end of reads (0)
.TP
\fB\-\-phred33\fR
qualities are Phred+33 (default)
.TP
\fB\-\-phred64\fR
qualities are Phred+64
.TP
\fB\-\-int\-quals\fR
qualities encoded as space\-delimited integers
.TP
\fB\-\-ignore\-quals\fR
treat all quality values as 30 on Phred scale (off)
.TP
\fB\-\-nofw\fR
do not align forward (original) version of read (off)
.TP
\fB\-\-norc\fR
do not align reverse\-complement version of read (off)
.SS "Classification:"
.TP
\fB\-\-min\-hitlen\fR <int>
minimum length of partial hits (default 22, must be greater than 15)
.TP
\fB\-\-min\-totallen\fR <int>
minimum summed length of partial hits per read (default 0)
.HP
\fB\-\-host\-taxids\fR <taxids> comma\-separated list of taxonomic IDs that will be preferred in classification
.HP
\fB\-\-exclude\-taxids\fR <taxids> comma\-separated list of taxonomic IDs that will be excluded in classification
.IP
Output:
.TP
\fB\-\-out\-fmt\fR <str>
define output format, either 'tab' or 'sam' (tab)
.TP
\fB\-\-tab\-fmt\-cols\fR <str>
columns in tabular format, comma separated
default: readID,seqID,taxID,score,2ndBestScore,hitLength,queryLength,numMatches
.TP
\fB\-t\fR/\-\-time
print wall\-clock time taken by search phases
.TP
\fB\-\-un\fR <path>
write unpaired reads that didn't align to <path>
.TP
\fB\-\-al\fR <path>
write unpaired reads that aligned at least once to <path>
.TP
\fB\-\-un\-conc\fR <path>
write pairs that didn't align concordantly to <path>
.TP
\fB\-\-al\-conc\fR <path>
write pairs that aligned concordantly at least once to <path>
.IP
(Note: for \fB\-\-un\fR, \fB\-\-al\fR, \fB\-\-un\-conc\fR, or \fB\-\-al\-conc\fR, add '\-gz' to the option name, e.g.
\fB\-\-un\-gz\fR <path>, to gzip compress output, or add '\-bz2' to bzip2 compress output.)
\fB\-\-quiet\fR               print nothing to stderr except serious errors
\fB\-\-met\-file\fR <path>     send metrics to file at <path> (off)
\fB\-\-met\-stderr\fR          send metrics to stderr (off)
\fB\-\-met\fR <int>           report internal counters & metrics every <int> secs (1)
.IP
Performance:
.HP
\fB\-o\fR/\-\-offrate <int> override offrate of index; must be >= index's offrate
.HP
\fB\-p\fR/\-\-threads <int> number of alignment threads to launch (1)
.TP
\fB\-\-mm\fR
use memory\-mapped I/O for index; many instances can share
.IP
Other:
.TP
\fB\-\-qc\-filter\fR
filter out reads that are bad according to QSEQ filter
.TP
\fB\-\-seed\fR <int>
seed for random number generator (0)
.HP
\fB\-\-non\-deterministic\fR seed rand. gen. arbitrarily instead of using read attributes
.TP
\fB\-\-version\fR
print version information and quit
.TP
\fB\-h\fR/\-\-help
print this usage message
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.