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Strain-resolved classification and assembly primer

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strainr: Strain-resolved classification and assembly primer

Intro

Strainr is a k-mer based metagenomic classifier that uses k-mer distributions and a naive Bayesian classifier to assign strain labels to DNA sequences. Strainr
is fast - database creation and classification of a metagenomic sample takes only minutes and can be run on a laptop.

1. Building a database

The default method for database creation involves choosing a single species - this is most likely done after initial investigation of species-level classification.

python strainr_database.py --taxid [species-taxid] --out [database-name]

2. Classification

python strainr_classify.py --db [database-name] --out [output-directory] [fastq-file]

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