Centrifuger

About

Citation and support

How to cite Centrifuger, where the source lives, and how to get help.

Citing Centrifuger#

If Centrifuger contributes to work you publish, please cite the Genome Biology paper:

Song, L., Langmead, B. Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification. Genome Biology 25, 106 (2024). doi:10.1186/s13059-024-03244-4

The paper received the Best Paper Award at RECOMB 2024.

BibTeX#

bibtex
@article{song2024centrifuger,
  title   = {Centrifuger: lossless compression of microbial genomes for
             efficient and accurate metagenomic sequence classification},
  author  = {Song, Li and Langmead, Ben},
  journal = {Genome Biology},
  volume  = {25},
  number  = {1},
  pages   = {106},
  year    = {2024},
  doi     = {10.1186/s13059-024-03244-4}
}

Please also cite the source of the reference database you used — RefSeq, GTDB, NCBI nt/nr and the LLNL-curated core_nt (PMID 40111052) each have their own citation.

Support#

Questions, bug reports and feature requests belong on the issue tracker:

github.com/mourisl/centrifuger/issues

A report is much easier to act on when it includes:

  • the Centrifuger version and how it was installed (Bioconda or make from source);
  • the exact command you ran;
  • which index you used, and whether it was downloaded or self-built;
  • the first lines of the error output, and any message on standard error;
  • for classification problems, a few representative rows of the output.

The FAQ and troubleshooting page covers the questions that come up most often; it is worth a look before filing.

Source code and licence#

Centrifuger is developed in the open at github.com/mourisl/centrifuger.

Copyright © 2023–present, Li Song. The licence terms are in the LICENSE file of the repository.

  • Centrifuge — the predecessor whose index-building conventions and default report format Centrifuger follows.
  • GTDB — the Genome Taxonomy Database, source of the cfr_gtdb_r232 indexes.
  • Bioconda — the packaged distribution.

About this documentation#

This site is generated from Markdown sources in the website/content directory. Every page carries an Edit this page on GitHub link at the bottom; corrections and additions are welcome through the same repository as the code.

Edit this page on GitHub