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How to cite TORMES and the included software

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Narciso Martin Quijada edited this page Oct 7, 2021 · 2 revisions

TORMES is a pipeline that makes it easy to analyze whole genome sequencing data but just running one command. For TORMES to run, it uses different software that arer the backbone of TORMES and MUST be cited when using TORMES for your analysis.

In the output directory you selected for TORMES, you will find a citations.txt file once the analysis is ended. This file contains all the software used for your particular TORMES analysis.

For instance, when running: tormes -m Salmonella-metadata.txt --genera Salmonella -t 32 --filtering trimmomatic --assembler spades -o tormes-salmonella

It will generate the following citations.txt file: Please cite the following software and databases when using this data for your publication:

* TORMES, [N.M. Quijada *et al*., 2019](https://doi.org/10.1093/bioinformatics/btz220)
* GNU Parallel, [O. Tange, 2018](https://doi.org/10.5281/zenodo.1146014)
* Trimmomatic, [A.M. Bolger *et al*., 2014](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103590/)
* SPAdes, [A. Bankevich *et al*., 2012](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519/)
* QUAST, [A. Gurevich *et al*., 2013](https://www.ncbi.nlm.nih.gov/pubmed/23422339)
* Barrnap, [T. Seemann](https://github.com/tseemann/barrnap)
* Kraken2, [Wood *et al*., 2019](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1891-0)
* RDP Classifier, [Q. Wang *et al*., 2007](https://aem.asm.org/content/73/16/5261)
* mlst, [T. Seemann](https://github.com/tseemann/mlst)
* ABRicate, [T. Seemann](https://github.com/tseemann/abricate)
* ResFinder database, [E. Zankari *et al*., 2012](https://www.ncbi.nlm.nih.gov/pubmed/22782487)
* CARD database, [A.G. McArthur *et al*., 2013](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3697360/)
* ARG-ANNOT database, [S.K. Gupta *et al*., 2014](https://www.ncbi.nlm.nih.gov/pubmed/24145532)
* VFDB database, [L. Chen *et al*., 2005](https://www.ncbi.nlm.nih.gov/pubmed/15608208)
* Prodigal, [Hyatt *et al*., 2010](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848648/)
* Prokka, [T. Seemann, 2014](https://www.ncbi.nlm.nih.gov/pubmed/24642063)
* Roary, [A.J. Page *et al*., 2015](https://www.ncbi.nlm.nih.gov/pubmed/26198102)
* SISTR, [C.E. Yoshida *et al*., 2016](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101)
* PlasmidFinder database, [A. Carattoli *et al*., 2014](https://www.ncbi.nlm.nih.gov/pubmed/24777092)
* PointFinder, [E. Zankari *et al*., 2017](https://www.ncbi.nlm.nih.gov/pubmed/29091202)

As an example of how to include this citations in your publication, you can write something as the following:


The analysis on whole genome sequencing data was performed by using TORMES vX.X.X (N.M. Quijada et al., 2019) as follows: quality filtering of the reads was performed by using Trimmomatic and assembled by using SPAdes (A.M. Bolger et al., 2014). Assembly statistics was performed by using QUAST (A. Gurevich et al., 2013). rRNA genes were extracted from the assembly by using Barrnap (T. Seemann) and taxonomically classified by using the RDP Classifier (Q. Wang et al., 2007). Kraken2 (Kraken2, Wood et al., 2019) was also used to infer the taxonomy of each sample. Multi-locus sequence typing (MLST) was performed by using mlst (T. Seemann). Salmonella in silico typing was performed by using SISTR (C.E. Yoshida et al., 2016). The screening of antimicrobial resistance genes was performed by using ABRicate (T. Seemann) against the ResFinder (E. Zankari et al., 2012), CARD (A.G. McArthur et al., 2013) and ARG-ANNOT (S.K. Gupta et al., 2014) databases. Additionally, antimicrobial resistances due to point mutations were investigated by using PointFinder. (E. Zankari et al., 2017) Virulence genes screening was performed by using ABRicate against the Virulence Factors Database (VFDB) (L. Chen et al., 2005). Gene prediction and annotation were performed by using Prodigal (Hyatt et al., 2010) and Prokka (T. Seemann, 2014). Pangenome comparison between the samples was conducted by using Roary (A.J. Page et al., 2015). The presence of plasmidic replicons in the samples was investigated by using ABRicate against the PlasmidFinder database (A. Carattoli et al., 2014). The GNU Parallel tool (O. Tange, 2018) was used for the parallelization of processes and the optimization of the computing strengths.

* Please add the versions of each software, which you can get from the terminal after activating TORMES environment (usually by adding the flag -v or --version). For instance: tormes --version

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