Pipeline_12

This is a bioinformatics pipeline for analyzing unfixed variants in Mycobacterium tuberculosis.

This pipeline is modified from the following repositories:

https://gitlab.com/tbgenomicsunit/ThePipeline https://github.com/MtbEvolution/resR_Project

Requirements

• Conda
• Nextflow
• R

Installation

Clone this repository:

git clone https://github.com/HDBigfoot/Pipeline_12.git

Usage

Running main pipeline:

nextflow run /PATH/TO/PROJECT/Pipeline_12/Pipeline_12-main.nf --raw_read1 /PATH/TO/RAW/READS/<sample_name>_1.fastq.gz --raw_read2 /PATH/TO/RAW/READS/<sample_name>_2.fastq.gz --sample_name <sample_name> --outdir <outdir>

References

ThePipeline:

Bermudez-Hernández, G.A., Pérez-Martínez, D.E., Madrazo-Moya, C.F. et al. Whole genome sequencing analysis to evaluate the influence of T2DM on polymorphisms associated with drug resistance in M. tuberculosis. BMC Genomics 23, 465 (2022). https://doi.org/10.1186/s12864-022-08709-z

resR:

Qingyun Liu et al., Tuberculosis treatment failure associated with evolution of antibiotic resilience. Science 378,1111-1118(2022). https://doi.org/10.1126/science.abq2787

Nextflow:

Di Tommaso, P., Chatzou, M., Floden, E. et al. Nextflow enables reproducible computational workflows. Nat Biotechnol 35, 316–319 (2017). https://doi.org/10.1038/nbt.3820

Main Pipeline

fastp

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

bwa-mem

Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997. 2013. https://doi.org/10.48550/arXiv.1303.3997

gatk4

Van der Auwera GA, O'Connor BD. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. 1st ed. O'Reilly Media; 2020.

samtools

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. https://doi.org/10.1093/bioinformatics/btp352

varscan

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009 Sep 1;25(17):2283-5. https://doi.org/10.1093/bioinformatics/btp373

Regions masked according to Marin, et al., (2022)

Maximillian Marin, Roger Vargas, Michael Harris, Brendan Jeffrey, L Elaine Epperson, David Durbin, Michael Strong, Max Salfinger, Zamin Iqbal, Irada Akhundova, Sergo Vashakidze, Valeriu Crudu, Alex Rosenthal, Maha Reda Farhat, Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome, Bioinformatics, Volume 38, Issue 7, March 2022, Pages 1781–1787, https://doi.org/10.1093/bioinformatics/btac023

snpEff

Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012 Apr-Jun;6(2):80-92. https://doi.org/10.4161/fly.19695