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The tormes report files

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Narciso M. Quijada edited this page Sep 11, 2020 · 12 revisions

under development


Once TORMES analysis ends, the results will be summarized in an interactive html-file, that is automatically performed by the tormes-report script included in TORMES environment. The report file (tormes_report.html) can be viewed in any web browser (if some browser return problems, please try to open it with a different one) and does not require any other data to be visualized, so the results can be easily visualized by different people just by sharing the tormes_report.html file. All the tables and figures included in the report file are downloadable.

However, probably the report is not showing exactly what you want or need. Additionally, you may have extra results, figures and tables that you would like to include before sharing with others. Or perhaps, you might want to modify some of the tables and/or figures that are already present in the report.

This is totally possible!

Some experience in R and R markdowns is needed, but we will try to make it easy through this wiki. Let's go step by step:


The report_files directory


After TORMES run, all the results generated and intermediate files will be contained in the output directory specified when running TORMES (see https://github.com/nmquijada/tormes#output for further information).
Inside this output directory, you will find a zipped directory: report_files.tgz. This directory contains all the files that were required to render the tormes_report.html. The information contained in this directory is redundant, as several results from other directories (antibiotic_resistance_genes, mlst, etc.) are copied into this directory. This is done intentionally, as the unzipped report_files.tgz can be used as the working directory for the user to easily modify the report. The directory is zipped in order to ocupy the less space as possible.

For unzipping report_files.tgz, type:

tar xzf report_files.tgz

Now, a directory (report_files) will appear and the zipped report_files.tgz will remain too. By looking to the content of the report_files directory, you will find the following files (I will sort them in this wiki according to their appearence possition in the tormes_report.html):

Samples description

  • metadata.txt: the same information that was parsed to the -m/--metadata option in TORMES).

Assembly analysis

  • sequencing_assembly_report.txt: contains the information regarding the sequencing and the assembly, generated by Quast and custom scripts.

Taxonomic identification

  • taxonomic-identification-kraken2.txt: contains the taxonomic identification results based on k-mers generated by Kraken2.
  • taxonomic-identification-16S-rRNA.RDP.txt: contains the taxonomic identification results based on the 16S rRNA gene generated by the RDP Classifier.

Multi-Locus Sequence Typing (MLST)

  • mlst.tab: contains the data generated by mlst.

Pangenome analysis

  • summary_statistics.txt: contains the number of core, soft, shell and cloud genes identified in your set of isolates, based on their prevalence within the different isolates. Generated by Roary.
  • pangenome.png: image that summarizes the gene composition of each isolate. Generated by roary2svg.pl.
  • accessory_binary_genes.fa.newick: newick file with the information of the pangenome tree based on presence/absence of genes between the isolates. Generated by Roary.
  • core_gene_alignment.newick: newick file with the information of pangenome tree based on core-genome-SNP distances. Generated by Roary.

Antibiotic resistance

  • *_argannot.tab: one file per isolate. Contains the results of the antibiotic resistance genes screening of that isolate against the ARG-ANNOT database. Generated by ABRicate.
  • *_card.tab: une file per isolate. Contains the results of the antibiotic resistance genes screening of that isolate against the CARD database. Generated by ABRicate.
  • *_resfinder.tab: une file per isolate. Contains the results of the antibiotic resistance genes screening of that isolate against the RESFINDER database. Generated by ABRicate.
  • argannot_summary.tab: matrix containing the presence/absence of the antibiotic resistance genes (from the ARG-ANNOT database) in the different isolates (coverage and identity > 90%). The value correspond to the % of identity. Generated by ABRicate and custom scripts included in tormes-report.
  • card_summary.tab: matrix containing the presence/absence of the antibiotic resistance genes (from the CARD database) in the different isolates (coverage and identity > 90%). The value correspond to the % of identity. Generated by ABRicate and custom scripts included in tormes-report.
  • resfinder_summary.tab: matrix containing the presence/absence of the antibiotic resistance genes (from the RESFINDER database) in the different isolates (coverage and identity > 90%). The value correspond to the % of identity. Generated by ABRicate and custom scripts included in tormes-report.

Virulence genes

  • *_vfdb.tab: one file per isolate. Contains the results of the virulence genes screening of that isolate against the VFDB database. Generated by ABRicate.

Additionally, if used the option -g/--genera Salmonella when running TORMES, you will also get:

Serotyping

  • serotyping.txt: serotyping results by using SISTR

Antibiotic resistance due to point mutations

  • *_PointFinder_results.txt: one file per isolate. Contain the results of point mutations known related to antimicrobial resistant. Generated with PointFinder

Plasmid replicons:

  • *_plasmids.tab: one file per isolate. Contains the results of the plasmid replicons screening of that isolate against the PlasmidFinder database. Generated by ABRicate.

And finally, three additional files generated by TORMES:

  • render_report.sh
  • tormes_report.html
  • tormes_report.Rmd
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