NAME
centrifuge - rapid and memory-efficient system for classification of DNA sequences
DESCRIPTION
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
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.