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.