In this Software Deep Dive episode, we talk with Dr. Bede Constantinides (University of Birmingham) about Deacon, a tool for removing host DNA reads from metagenomic datasets. We discuss why host read removal is a deceptively difficult problem, the limitations of alignment-based approaches, and how Deacon evolved from Bede's earlier tool Hostile.

The conversation covers practical issues such as human contamination in metagenomes, balancing sensitivity vs specificity when filtering reads, and the computational challenges of working with large human reference datasets and pangenomes.

This episode focuses on the background and motivation for Deacon. The next episode will dive deeper into how the method works.

Links

Deacon

https://github.com/bede/deacon

Hostile

https://github.com/bede/hostile/

Bede Constantinides

http://bede.im/

nf-core taxprofiler

https://nf-co.re/taxprofiler

Kraken2

https://ccb.jhu.edu/software/kraken2/