Introduction

UNIFESPntmnewspecies_nf is a bioinformatics pipeline used for the paper entitled Description of new species of Mycobacterium terrae complex isolated from sewage at the São Paulo Zoological Park Foundation in Brazil

IDs for the submitted FASTQ samples

| Sample ID | ATCC ID | JCM ID | Nomenclature | Nomenclature alias (Gupta et a. 2018) | GenBanK 16S rRNA gene | Bioproject | Biosample | SRA | GenBank Draft Genome | PGAP Annotation | |:---------:|:--------:|:------:|:-------------------------:|:-------------------------------------:|:---------------------:|:-----------:|:------------:|:-----------:|:--------------------:|:---------------:| | MYC017 | TSD-296T | 35364T | Mycobacterium vasticus | Mycolicibacter vasticus | MK890459.1 | PRJNA755977 | SAMN20959233 | SRR27405758 | CP084028 | JAYJJQ000000000 | | MYC098 | TSD-297T | 35365T | Mycobacterium crassicus | Mycolicibacter crassicus | MK890478.1 | PRJNA757362 | SAMN20959234 | SRR27405950 | CP084029 | JAYJJR000000000 | | MYC101 | TSD-298T | 35366T | Mycobacterium zoologicum | Mycolicibacter zoologicum | MK890479.1 | PRJNA757364 | SAMN20959235 | SRR27405954 | CP084030 | JAYJJS000000000 | | MYC123 | BAA3216 | 35367 | Mycobacterium zoologicum | Mycolicibacter zoologicum | MK890481.1 | PRJNA743883 | SAMN20062777 | SRR27406169 | CP083985 | JAYJJT000000000 | | MYC340 | TSD-299T | 35368T | Mycobacterium nativiensis | Mycolicibacter nativiensis | MK890521.1 | PRJNA743885 | SAMN20062778 | SRR27406220 | CP083986 | JAYJJU000000000 |

Usage

Note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

bash nextflow run emilyncosta/UNIFESP_ntm_newspecies_nf \ -profile docker \ --input samplesheet.csv \ --outdir <OUTDIR>

Warning: Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

UNIFESPLABMICOBACT/ntmmterrae_nf was originally written by Abhinav Sharma (@abhi18av).

We thank the following people for their extensive assistance in the development of this pipeline: Luciano Antonio Digiampietri (@digiampietri), Edson Filho Machado Silvia (@edsonmachado) and Emilyn Costa Conceicao (@emilyncosta)

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

This pipeline is part of the following study: Romagnoli et al. 2024. Description of new species of Mycobacterium terrae complex isolated from sewage at the São Paulo Zoological Park Foundation in Brazil https://www.frontiersin.org/articles/10.3389/fmicb.2024.1335985

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.