This section includes links to tools and resources developed by the funded projects under various JPIAMR calls.
Click on the arrows next to each heading to sort by call, project or tool name.
| Call | Project | Tool | Description |
|---|---|---|---|
| Transmission Dynamics | DARWIN | Plaspline | A pipeline for plasmid analysis form metagenome. |
| Transmission Dynamics | STARCS | mlplasmids | Consists of binary classifiers to predict contigs either as plasmid-derived or chromosome-derived. |
| Transmission Dynamics | STARCS | gplas | A tool to bin plasmid-predicted contigs based on sequence composition, coverage and assembly graph information. |
| Transmission Dynamics | STARCS | RFPlasmid | Predicting plasmid contigs from assemblies. |
| Transmission Dynamics | STARCS | ResCap | Repository for software, raw data tables and data bases. |
| Transmission Dynamics | STARCS | PATO | A R package designed to analyze pangenomes (set of genomes) intra or inter species. |
| Transmission Dynamics | STARCS | MetaTOR | Metagenomic Tridimensional Organisation-based Reassembly – A set of scripts that streamlines the processing and binning of metagenomic metaHiC datasets. |
| Transmission Dynamics | SpARK | Pathogen Watch database | Genome reference data for Klebsiella genus. |
| Transmission Dynamics | SpARK | mSWEEP software | Fast and accurate bacterial community composition estimation on strain level by using pseudoalignments and variational inference. |
| Transmission Dynamics | ST131TS | Bioinformatic freetware-AccNET | A comparative genomic tool for accessory genome analysis using bipartite networks. |
| Transmission Dynamics | ST131TS | PATO | Pangenome Analysis Toolkit |
| Transmission Dynamics | PREPARE | inferenceFitnessLandscape | Statistical method for fitness landscape inference from experimental evolution data |
| Transmission Dynamics | PREPARE | empiricIST | Statistical method for analysis of deep mutational scanning fitness data |
| Transmission Dynamics | MACOTRA | Blast taxon resolver | Novel algorithm and software to improve precision of DNA metabarcoding in microbiota analyses |
| Transmission Dynamics | MACOTRA | strain_growth | Dehydration model |
| Transmission Dynamics | MACOTRA | MACOTRA strain collection metadata database | MACOTRA strain collection metadata database |
| Transmission Dynamics | JumpAR | SMART database | The MGE recombinase sequence models (HMMs) generated in this study are available for public access with SMART database. |
| Transmission Dynamics | JumpAR | NeighborsScan | Computational pipeline for functional annotation of MGErelated tyrosine recombinases. |
| Transmission Dynamics | HECTOR | NCBI BioProject | Whole-genome sequencing data of 1198 strains, together with metadata. |
| Transmission Dynamics | BEAT-AMR | Special microfluidic device for biofilm formation | Biofilm flow chamber design linked to a publicly available platform to analyse molecular or evolutionary mechanisms of biofilm-associated antimicrobial resistance using microfluidics, genomics, transcriptomics, proteomics and proteogenomics. |
| Transmission Dynamics | BEAT-AMR | iPtgxDB | An integrated proteogenomics search database (iPtgxDB) for Pseudomonas aeruginosa strain MPAO1 |
