Documentation

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coproID (COprolite IDentification) is a tool developed at the Max Planck insitute for the Science of Human History by Maxime Borry

The purpose of coproID is to help identify the host of given sequenced microbiome when there is a doubt between species.

coproID is a pipeline developed using Nextflow

and made available through nf-core

Even though it was developed with coprolite host identification in mind, it can be applied to any microbiome, provided they contain host DNA.

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

Quick start

Example:

nextflow run maxibor/coproid --genome1 'GRCh37' --genome2 'CanFam3.1' --name1 'Homo_sapiens' --name2 'Canis_familiaris' --reads '*_R{1,2}.fastq.gz'

coproID example workFlow

dag

How to cite coproID

The coproID article is coming.