TB/NTM species identification pipeline Version 1.0 (beta)¶

Short Description¶

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.

Authors code¶

J.P.M. Coolen
H. Severin

Tool References¶

fastp

Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560

centrifuge

https://ccb.jhu.edu/software/centrifuge/manual.shtml

KMA

Clausen, P.T.L.C., Aarestrup, F.M. & Lund, O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 19, 307 (2018). https://doi.org/10.1186/s12859-018-2336-6

SNP-IT

Lipworth S, Jajou R, de Neeling A, et al. SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex. Emerging Infectious Diseases. 2019;25(3):482-488. doi:10.3201/eid2503.180894.

gatk

Van der Auwera GA & O'Connor BD. (2020). Genomics in the Cloud: Using Docker, GATK, and WDL in Terra (1^st Edition). O'Reilly Media.

bwa-mem

Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]

delly

Tobias Rausch, Thomas Zichner, Andreas Schlattl, Adrian M. Stuetz, Vladimir Benes, Jan O. Korbel. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012 Sep 15;28(18):i333-i339. https://doi.org/10.1093/bioinformatics/bts378

Citation¶

Currently in submission fase:

MGIT enriched shotgun metagenomics for routine identification of nontuberculous mycobacteria: a route to personalized healthcare

Jodie A. Schildkraut1*, Jordy P.M. Coolen1*, Heleen Severin1, Ellen Koenraad1, Nicole Aalders1, Willem J.G. Melchers1, Wouter Hoefsloot2, Heiman F.L. Wertheim1, Jakko van Ingen1
1)  Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
2)  Radboudumc Center for Infectious Diseases, Department of pulmonary diseases, Radboud University Medical Center, Nijmegen, the Netherlands

*Authors contributed equally