Project tools

This section includes links to tools and resources developed by the funded projects under various JPIAMR calls.

Call Name 2019 - Call on Diagnostics and Surveillance 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
Call Name 2016 - Transmission Dynamics Project Acronym PATO Description Pangenome Analysis Toolkit	Tool Name ST 131_transmission
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
Call Name 2016 - Transmission Dynamics Project Acronym strain_growth Description Dehydration model	Tool Name MACOTRA
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

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