GitHub Pages

Author: Jordy Coolen

Projects

EasySeq RC-PCR SARS-CoV-2

This github repository contains an automated pipeline dedicated to properly analyse the EasySeq SARS-CoV-2 (COVID-19) sequence sequencing data. Validated with 150/151 bp paired-end reads.

Scientific paper:

Coolen, J. P., Wolters, F., Tostmann, A., van Groningen, L. F., Bleeker-Rovers, C. P., Tan, E. C., ... & Melchers, W. J. (2021). SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis. Journal of Clinical Virology, 144, 104993. https://doi.org/10.1016/j.jcv.2021.104993

MyCodentifier

The pipeline is constructed using nextflow as workflow manager running in a docker container. It is able to identify species of TB/nTM from positive MGIT cultures. To do so it uses a hsp65 database for fast identification coupled with a Metagenomic method using centrifuge to identify on genome level. For TB it also is able to identify subspecies. Results are presented in automated pdf and html reports.

Scientific paper:

Schildkraut JA, Coolen JPM, Severin H, Koenraad E, Aalders N, Melchers WJG, Hoefsloot W, Wertheim HFL, van Ingen J. MGIT Enriched Shotgun Metagenomics for Routine Identification of Nontuberculous Mycobacteria: a Route to Personalized Health Care. J Clin Microbiol. 2023 Feb 22:e0131822. doi: 10.1128/jcm.01318-22. Epub ahead of print. PMID: 36840602.

RC-PCR Classifier

Reverse complement-PCR pipeline for 16S RC-PCR assay analysis. Compatible with the EasySeq™ 16S rRNA Bacterial ID Kit.

New early in development

BasicPhylo