|Bacteria, Archaea (compressed)||4.4 GB|
|Bacteria, Archaea, Viruses, Human (compressed)||5.4 GB|
|Bacteria, Aarchaea, Viruses, Human||7.9 GB|
|NCBI nucleotide non-redundant sequences||50 GB|
Kim D, Song L, Breitwieser FP, and Salzberg SL. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research 2016
Have a look at https://github.com/fbreitwieser/pavian for visual analysis of results generated with Centrifuge!
Centrifuge 1.0.3-beta release 12/06/2016
- Fixed Perl hash bangs (thanks to Andreas Sjödin / @druvus).
- Updated nt database building to work with new accession code scheme.
- Added option --tab-fmt-cols to specify output format columns.
- A minor fix for traversing the hitmap up the taxonomy tree.
Centrifuge paper published at Genome Research 11/16/2016
Centrifuge 1.0.2-beta release 5/25/2016
- Fixed a runtime error during abundance analysis.
- Changed a default report file name from centrifuge_report.csv to centrifuge_report.tsv.
Centrifuge preprint is available here at bioRxiv 5/24/2016
Centrifuge 1.0.1-beta release 3/8/2016
Centrifuge is now able to work directly with SRA data: both downloaded on demand over internet and prefetched to local disks.
For example, you can run Centrifuge with SRA data (SRR353653) as follows.
centrifuge -x /path/to/index --sra-acc SRR353653
- This eliminates the need to download SRA reads manually and to convert them into fasta/fastq format without affecting the run time.
- For example, you can run Centrifuge with SRA data (SRR353653) as follows.
- We provide a Centrifuge index (nt index) for NCBI nucleotide non-redundant sequences collected from plasmids, organelles, viruses, archaea, bacteria, and eukaryotes, totaling ~109 billion bps. Centrifuge is a very good alternative to Megablast (or Blast) for searching through this huge database.
- Fixed Centrifuge's scripts related to sequence downloading and index building.
Centrifuge 1.0.0-beta release 2/19/2016 - first release
- The first release of Centrifuge features a dramatically reduced database size, higher classification accuracy and sensitivity, and comparably rapid classification speed.
- Please refer to the manual for details on how to run Centrifuge and interpret Centrifuge’s classification results.
We provide several standard indexes designed to meet the needs of most users (see the side panel - Indexes)
- For compressed indexes, we first combined bacterial genomes belonging to the same species and removed redundant sequences, and built indexes using the combined sequences. As a result, those compressed indexes are much smaller than uncompressed indexes. Centrifuge classifies reads at the species level when using the compressed indexes and at the strain level (or the genome level) when using the uncompressed indexes.