This section includes links to tools and resources developed by the funded projects under various JPIAMR calls.
Project Acronym ResFinderFG v2.0 Description A database of antibiotic resistance genes obtained by functional metagenomics |
Tool Name EMBARK |
Call Name 2018 - Innovations against antibiotic-resistant bacteria: New targets, compounds and tools Project Acronym 2FAST2Q Description A general-purpose sequence search and counting program for FASTQ files. |
Tool Name DISRUPT |
Call Name 2016 - Transmission Dynamics Project Acronym Plaspline Description A pipeline for plasmid analysis form metagenome. |
Tool Name DARWIN |
Call Name 2016 - Transmission Dynamics Project Acronym mlplasmids Description Consists of binary classifiers to predict contigs either as plasmid-derived or chromosome-derived. |
Tool Name STARCS |
Call Name 2016 - Transmission Dynamics Project Acronym gplas Description A tool to bin plasmid-predicted contigs based on sequence composition, coverage and assembly graph information. |
Tool Name STARCS |
Call Name 2016 - Transmission Dynamics Project Acronym RFPlasmid Description Predicting plasmid contigs from assemblies. |
Tool Name STARCS |
Call Name 2016 - Transmission Dynamics Project Acronym ResCap Description Repository for software, raw data tables and data bases. |
Tool Name STARCS |
Call Name 2016 - Transmission Dynamics Project Acronym PATO Description A R package designed to analyze pangenomes (set of genomes) intra or inter species. |
Tool Name STARCS |
Call Name 2016 - Transmission Dynamics Project Acronym MetaTOR Description Metagenomic Tridimensional Organisation-based Reassembly – A set of scripts that streamlines the processing and binning of metagenomic metaHiC datasets. |
Tool Name STARCS |
Call Name 2016 - Transmission Dynamics Project Acronym Bioinformatic freetware-AccNET Description A comparative genomic tool for accessory genome analysis using bipartite networks. |
Tool Name ST 131_transmission |
Tool Name ST 131_transmission |
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Call Name 2016 - Transmission Dynamics Project Acronym Pathogen Watch database Description Genome reference data for Klebsiella genus. |
Tool Name SpARK |
Call Name 2016 - Transmission Dynamics Project Acronym mSWEEP software Description Fast and accurate bacterial community composition estimation on strain level by using pseudoalignments and variational inference. |
Tool Name SpARK |
Call Name 2016 - Transmission Dynamics Project Acronym inferenceFitnessLandscape Description Statistical method for fitness landscape inference from experimental evolution data |
Tool Name PREPARE |
Call Name 2016 - Transmission Dynamics Project Acronym empiricIST Description Statistical method for analysis of deep mutational scanning fitness data |
Tool Name PREPARE |
Call Name 2016 - Transmission Dynamics Project Acronym Blast taxon resolver Description Novel algorithm and software to improve precision of DNA metabarcoding in microbiota analyses |
Tool Name MACOTRA |
Tool Name MACOTRA |
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Call Name 2016 - Transmission Dynamics Project Acronym MACOTRA strain collection metadata database Description MACOTRA strain collection metadata database |
Tool Name MACOTRA |
Call Name 2016 - Transmission Dynamics Project Acronym SMART database Description The MGE recombinase sequence models (HMMs) generated in this study are available for public access with SMART database. |
Tool Name JumpAR |
Call Name 2016 - Transmission Dynamics Project Acronym NeighborsScan Description Computational pipeline for functional annotation of MGErelated tyrosine recombinases. |
Tool Name JumpAR |
Call Name 2016 - Transmission Dynamics Project Acronym NCBI BioProject Description Whole-genome sequencing data of 1198 strains, together with metadata. |
Tool Name HECTOR |
Call Name 2016 - Transmission Dynamics Project Acronym Special microfluidic device for biofilm formation Description 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. |
Tool Name BEAT-AMR |
Call Name 2016 - Transmission Dynamics Project Acronym iPtgxDB Description An integrated proteogenomics search database (iPtgxDB) for Pseudomonas aeruginosa strain MPAO1 |
Tool Name BEAT-AMR |