ISHAM Fungal WGS protocol benchmarking

Comparison of genomic variant identification protocols for Candidas auris

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Background

This is a consortium effort from the International Society for Human and Animal Mycology (ISHAM) community, with 11 independent groups across four continents, for the aim of establishing a best practice of genomic variant identification pipeline. For convenors and members of the working group, check below.

Repository

This is a repository with data and analysis script needed to reproduce most of the analyses benchmarking genomic variant identification protocols for the fungal community.

The repository was structured as follows:

• data: data needed
• figs: figures reproduced from the jupyter notebook.
• analysis.ipynb: jupyter notebook to reproduce results from the corresponding manuscript.
• README.md: this file.

Usage & Dependencies

To reproduce figures from the manuscript, make sure the following tools are available

• Python >= 3.4
• pip3 >=20.1.1

Install the following python 3 packages via pip:

pip install statistics matplotlib pandas numpy funpipe=0.1.0 jupyter

Clone this repo:

git clone git://github.com/broadinstitute/isham_wgs.git
cd isham_wgs
jupyter notebook analysis.ipynb

Note that additional tools and the raw VCF files are needed to reproduce the analysis from scratch, including:

• vcftools-v0.1.15
• zlib-1.2.11
• bcftools-v1.8
• htslib-v1.10.2 (bgzip and tabix)

Uncomment bash sections of the notebook to fully reproduce the analysis.

Data Availability

All raw data's submitted to NCBI. Important outputs are shared in this figshare project. Check here for paths to the submitted files from all 12 groups.

Working group: Genomic Epidemiology of Fungal Infections

Overview, Achievements and Publications

Convenor(s)

• Christina Cuomo (cuomo@broadinstitute.org)
• Anastasia Litvintseva (frq8@cdc.gov)
• Ana Alastruey-Izquierdo (anaalastruey@isciii.es)
• Matthew Fisher (matthew.fisher@imperial.ac.uk)
• David Engelthaler (dengelthaler@tgen.org)

Citation

To citate this work, use the following:

Li X, Muñoz JF, Gade L, Argimon S, Bougnoux ME, Bowers JR, Chow NA, Cuesta I, Farrer RA, Maufrais C, Monroy-Nieto J, Pradhan D, Uehling J, Vu D, Yeats CA, Aanensen DM, d'Enfert C, Engelthaler DM, Eyre DW, Fisher MC, Hagen F, Meyer W, Singh G, Alastruey-Izquierdo A, Litvintseva AP, Cuomo CA. Comparing genomic variant identification protocols for Candida auris. Microb Genom. 2023 Apr;9(4). doi: 10.1099/mgen.0.000979. PMID: 37043380.

Issues

Contact Xiao Li (xiaoli@broadinstitute.org) if you have any analysis related questions. Submit an issue for bugs.