NGS Taxon - a generic module for read taxonomic asignment

This module implements read taxonomic assignment steps:

• Map reads agains reference collection
  • Bowtie2 / BWA_aln
• Remove saturated reads
• Clean header for unused references
• Reassign reads
  • bam-filter
• Filter BAM references
  • bam-filter
• Taxonomic assignment
  • metaDMG

And QC steps:

• MultiQC (aggregates QC from several of the tools above)
  • Samtools Stats

This module can be used directly, but is designed to be used together with other modules.

Authors

• Filipe G. Vieira

Usage

For an example on how to use this module, check repo aeDNA.