A program to estimate microbial richness from metagenomic sequencing data by counting k-mers
Project description
ESKRIM: EStimate with K-mers the RIchness in a Microbiome
Purpose
- ESKRIM is a reference-free tool that compares microbial richness in shotgun metagenomic samples by counting k-mers
Installation via pip
pip install eskrim
Usage
eskrim -h
Contaminants reads from the host genome should be removed before using ESKRIM.
If your FASTQ files are paired, we recommend to use only forward reads.
Authors
- Florian Plaza Oñate: florian.plaza-onate@inrae.fr
- Emmanuelle Le Chatelier: emmanuelle.le-chatelier@inrae.fr
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