Creating Snakemake pipeline for metagenomics classifier tool: Centrifuge for Oxford Nanopore reads.

Centrifuge is microbial classification tools used for rapid and accurate labeling of reads and there classification.
Centrifuge use Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index method to classify microbial community.
For classification of species usually alignment is not needed, therefore for classification, indxes are build with large set of target genomes.
For this centrifuge version 1.0.4 is used to build indexes for Bacteria, Fungi, Virus and human gnomes.

Building index for Bacteria, fungi, virues

To build index centrifuge use following files:
- taxonomy/name.dmp file
- taxonomy/node.dmp file
- library/input_sequences.fna
- seqid2taxid.map
After building indexes it give outputs with suffixes .1.cf, 2..cf and so on.