A workflow for analyzing metagenomic samples. It assigns taxonomic labels to DNA sequences, estimates the abundance of the taxonomic categories in the sample, makes visualizations that give insights into the taxonomic structure of the sample, and makes files that are suitable for downstream analysis. This allows researchers to assign reads from their samples to a likely species of origin and quantify each species’ abundance.
A workflow that builds an index from reference sequences downloaded from NCBI databases.
Five tools from the Centrifuge 1.0.4 toolkit:
- Centrifuge Classifier is the main tool of the Centrifuge toolkit, used for classification of metagenomics reads.
- Centrifuge Download is a part of the Centrifuge toolkit, used for downloading reference sequences from NCBI.
- Centrifuge Build is a part of the Centrifuge toolkit, which makes a Centrifuge index from DNA sequences.
- Centrifuge Kreport is used to make a Kraken-style report from the Centrifuge Classifier output.
- Centrifuge Inspect is a part of the Centrifuge toolkit that inspects index files.