Pipeline_11

This is a bioinformatics pipeline I wrote for the analysis of Mycobacterium tuberculosis genomes for the Research Center for Care and Control of Infectious Diseases (RC3ID) and the Center for Translational Biomarker Research (CentraBioRes), Universitas Padjadjaran.

This pipeline is modified from Mycodentifier (https://github.com/JordyCoolen/MyCodentifier.git)

Requirements

• Conda
• Nextflow
• R
• Python

Installation

Clone this repository:

git clone https://github.com/HDBigfoot/Pipeline_11.git

Usage

Running main pipeline:

nextflow run /PATH/TO/PROJECT/Pipeline_11/Pipeline_11-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>

Combining and masking FASTAs:

nextflow run /PATH/TO/PROJECT/Pipeline_11/CombineAndMask.nf --sample_list <list-of-samples>.txt --inputdir /PATH/TO/FASTA/FILES/ --project_name <project_name>

Running SNP-Distance Analysis:

nextflow run /PATH/TO/PROJECT/Pipeline_11/SnpDistance.nf --input_fasta /PATH/TO/COMBINED/FASTA/<combined_fasta>.masked.fasta --project_name <project_name>

References

MyCodentifier:

Schildkraut JA, Coolen JPM, Severin H, Koenraad E, Aalders N, Melchers WJG, et al. MGIT Enriched Shotgun Metagenomics for Routine Identification of Nontuberculous Mycobacteria: a Route to Personalized Health Care. J Clin Microbiol. 2023 Mar 23;61(3):e0131822. https://doi.org/10.1128/jcm.01318-22

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.

Masking Fasta

Code for masking fastas was provided by Dr. Philip Ashton, regions masked as per (Holt, et al., 2018):

Holt, K.E., McAdam, P., Thai, P.V.K. et al. Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nat Genet 50, 849–856 (2018). https://doi.org/10.1038/s41588-018-0117-9

Seqkit

Shen W, Sipos B, Zhao L. SeqKit2: A Swiss army knife for sequence and alignment processing. iMeta. 2024;3(3):191. https://doi.org/10.1002/imt2.191.

Bedtools

Aaron R. Quinlan, Ira M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, Volume 26, Issue 6, March 2010, Pages 841–842, https://doi.org/10.1093/bioinformatics/btq033

SNP-Distance Analysis

snp-dists

https://github.com/tseemann/snp-dists.git