version 1.3.0

Improvements included in the novel version 1.3.0 of the TORMES pipeline:

• Specific analyses for Klebsiella by enabling the --genera Klebsiella option. The specific analyses include: plasmid detection by using PlasmidFinder, detection of point mutations associated with antimicrobial resistance by using PointFinder and subtyping of the isolates based on surface polysaccharide locus: complex capsule (K) and on complex LPS (O) locus by using Kaptive.
• Possibility to perform nucleotide gene searches from user custom databases (must be nucleotide databases as the search is based on BLASTN by using ABRicate) by using the --custom_genes_db option (for instance --custom_genes_db “mydb1 mydb2 mydb3). You can use as many custom databases as you want. The custom databases must have been previously formatted and installed in TORMES (see the instructions in the Wiki).
• You can set the maximum number of threads to use for genome assembly by using the --max_cpus_per_assembly option. For instance, if you set --threads 48 (which set the maximum number of threads for TORMES to use to 48) and --max_cpus_per_assembly 8, this will make TORMES to perform 6 assemblies in parallel by using 8 threads per assembly.
• Set the minimum contig length of your assemblies by using the --min_contig_len option (default=200).
• Possibility to modify the minimum percentage of coverage and identity of genes’ searches by using the --gene_min_cov and the --gene_min_id options, respectively (default = 80).
• Disable genome annotation by Prokka and just perform gene prediction with Prodigal (--only_gene_prediction option. Default=no)
• You can set further options to be parsed to Prodigal as a string after the --prodigal_options flag (it requires the --only_gene_prediction option to enabled).
• A “citation.txt” file will be created in your run including the citations of each of the software and databases that were used in your analysis (will also be included in the “Citations” section of the tormes-report). TORMES is a pipeline that rely on all the software included in each "citations.txt" file and we strongly encourage to cite them all when citing TORMES.
• The "DT" R package is now used for the tormes-report generation, which renders interactive tables in the tormes_report.html file.

version 1.2.1

This version fixes the following issues from version 1.2.0:

• #27 : report is now generated even there is no MLST scheme available for the isolate(s) (no need to use the --no_mlst option).
• #30 : fixed path of the automatically downloaded minikraken2 database in the "config_file.txt" when running tormes-setup.
• #31 : Perl package perl-try-tiny-retry included in the tormes-1.2.1.yml

version 1.2.0

Released in September 2020
New features: Kraken2 is now used instead of Kraken, increasing the sensitivity and speed for the taxonomic identification based on k-mers. Additionally, rRNA genes will be extracted from the genomes and the 16S rRNA genes will be used for taxonomic classification by using the RDP Classifier.

version 1.1

Released in April 2020.
New features: Enables the option to include already assembled genomes into the analysis, alone or in combination with raw sequencing data.

Original version of the TORMES pipeline

Original version of the TORMES pipeline, as published in Quijada et al. 2019.
Released in April 2019