Centrifuge¶
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.
Profile Format¶
A Kraken-style txt
output file produced by the centrifuge-kreport
auxiliary tool (a part of the Centrifuge package) is accepted by taxpasta
.
Column Header | Description |
---|---|
percent | |
clade_assigned_reads | |
direct_assigned_reads1 | |
taxonomy_level | |
taxonomy_id | |
name |
Example¶
0.00 0 0 U 0 unclassified
100.00 99 0 - 1 root
98.99 98 0 D 10239 Viruses
33.33 33 0 F 687329 Anelloviridae
23.23 23 1 G 687331 Alphatorquevirus
1.01 1 1 S 687340 Torque teno virus 1
1.01 1 1 S 687342 Torque teno virus 3
-
Value used in standardised profile output ↩