Classifying Billion base-pairs/second

Chillar Anand (avilpage.com)

Agenda

• What is meta-genomic analysis?
• Taxanomic classification tools
• Intro to Kraken2
• Speeding up Kraken2

What is Meta-Genomics?

Study of all organims in a community by their DNA.
Ex: Soil sample, gut microbiome, ocean water, etc.

Can a scoop of mud give you latitude/longitude?
Can we detect an outbreak in cities of before doctors?

Abundance Profile & Taxonomy

Sub-string search

Kraken2 Index

Faster Classification

References

• https://github.com/DerrickWood/kraken2

• https://github.com/hoytech/vmtouch

• https://avilpage.com/tags/kraken2.html

• https://pmc.ncbi.nlm.nih.gov/articles/PMC6716367/