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.