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.