CENTRIFUGE(1)

🦋 NAME 🦋

okay so bestie, meet centrifuge — a rapid and memory-efficient system for classification of DNA sequences 💅✨

🌸 DESCRIPTION 🌸

so this is Centrifuge version 1.0.3-beta, brought to you by the Centrifuge developer team (centrifuge.metagenomics@gmail.com) 🫶

here's the vibe, the usage, the whole ~thing~:

centrifuge [options]* -x <cf-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <filename>] [--report-file <report>]

and now, the cast of characters (a.k.a. the arguments, no skips, all of them):

• <cf-idx> — the index filename prefix, minus the trailing .X.cf. that's your starting point fr 💫
• <m1> — files with #1 mates, paired up with the files in <m2>. they can be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2) 🧚
• <m2> — files with #2 mates, paired up with the files in <m1>. also can be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2) 🧚
• <r> — files with unpaired reads. yep, gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2) allowed here too
• <filename> — the file for classification output (default: stdout)
• <report> — the file for tabular report output (default: centrifuge_report.tsv)

✨ lowkey iconic detail: <m1>, <m2>, and <r> can be comma-separated lists (no whitespace, bestie, none) and you can specify them many times. like, for example: -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 the 5'/left end of reads (0)
• -3/--trim3 <int> — trim <int> bases from the 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 the Phred scale (off)
• --nofw — do not align the forward (original) version of the read (off)
• --norc — do not align the reverse-complement version of the read (off)

🎀 Classification 🎀

• --min-hitlen <int> — minimum length of partial hits (default 22, and it must be greater than 15, ok? rules are rules 💀)
• --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 the 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 the 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>

🫶 heads up: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name — e.g. --un-gz <path> — to gzip compress the output, or add '-bz2' to bzip2 compress the output. that's the whole trick, no cap.

• --quiet — print nothing to stderr except serious errors 🤫
• --met-file <path> — send metrics to the 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 the offrate of the index; it must be >= the index's offrate 🚨
• -p/--threads <int> — number of alignment threads to launch (1)
• --mm — use memory-mapped I/O for the index; many instances can share it, cute and efficient ✨

🌈 Other 🌈

• --qc-filter — filter out reads that are bad according to the QSEQ filter
• --seed <int> — seed for the random number generator (0)
• --non-deterministic — seed the 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. 🫶

and that's the whole page, bestie — centrifuge version 1.0.3, dated October 2021. go classify something iconic 💅🎀✨