centrifuge - rapid and memory-efficient system for classification of DNA sequences

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

centrifuge 1.0.3                                  October 2021                                     CENTRIFUGE(1)

       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

       centrifuge - rapid and memory-efficient system for classification of DNA sequences