Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial genomes) yet provides very fast classification speed, allowing it to process a typical DNA sequencing run within an hour. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers.
Following is the manpage for centrifuge, which can be linked with the options above using the help text. Note that not all options are available in the Galaxy wrapper.
centrifuge [options]* -x <cf-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-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).
<SRA accession number> Comma-separated list of SRA accession numbers, e.g. --sra-acc SRR353653,SRR353654.
<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)
--sra-acc SRA accession ID
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 'bowtie's 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