Project tools

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

Project Acronym 2FAST2Q

Description A general-purpose sequence search and counting program for FASTQ files.

Tool Name DISRUPT

Project Acronym Plaspline

Description A pipeline for plasmid analysis form metagenome.

Tool Name DARWIN

Project Acronym mlplasmids

Description Consists of binary classifiers to predict contigs either as plasmid-derived or chromosome-derived.

Tool Name STARCS

Project Acronym gplas

Description A tool to bin plasmid-predicted contigs based on sequence composition, coverage and assembly graph information.

Tool Name STARCS

Project Acronym RFPlasmid

Description Predicting plasmid contigs from assemblies.

Tool Name STARCS

Project Acronym ResCap

Description Repository for software, raw data tables and data bases.

Tool Name STARCS

Project Acronym PATO

Description A R package designed to analyze pangenomes (set of genomes) intra or inter species.

Tool Name STARCS

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

Description A comparative genomic tool for accessory genome analysis using bipartite networks.

Tool Name ST 131_transmission

Project Acronym PATO

Description Pangenome Analysis Toolkit

Tool Name ST 131_transmission

Project Acronym Pathogen Watch database

Description Genome reference data for Klebsiella genus.

Tool Name SpARK

Project Acronym mSWEEP software

Description Fast and accurate bacterial community composition estimation on strain level by using pseudoalignments and variational inference.

Tool Name SpARK

Project Acronym inferenceFitnessLandscape

Description Statistical method for fitness landscape inference from experimental evolution data

Tool Name PREPARE

Project Acronym empiricIST

Description Statistical method for analysis of deep mutational scanning fitness data

Tool Name PREPARE

Project Acronym Blast taxon resolver

Description Novel algorithm and software to improve precision of DNA metabarcoding in microbiota analyses

Tool Name MACOTRA

Project Acronym strain_growth

Description Dehydration model

Tool Name MACOTRA

Description MACOTRA strain collection metadata database

Tool Name MACOTRA

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

Project Acronym NeighborsScan

Description Computational pipeline for functional annotation of MGErelated tyrosine recombinases.

Tool Name JumpAR

Project Acronym NCBI BioProject

Description Whole-genome sequencing data of 1198 strains, together with metadata.

Tool Name HECTOR

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

Project Acronym iPtgxDB

Description An integrated proteogenomics search database (iPtgxDB) for Pseudomonas aeruginosa strain MPAO1

Tool Name BEAT-AMR