Project tools

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.

CallProjectTool Description
Transmission DynamicsDARWINPlasplineA pipeline for plasmid analysis form metagenome.
Transmission DynamicsSTARCSmlplasmidsConsists of binary classifiers to predict contigs either as plasmid-derived or chromosome-derived.
Transmission DynamicsSTARCSgplasA tool to bin plasmid-predicted contigs based on sequence composition, coverage and assembly graph information.
Transmission DynamicsSTARCSRFPlasmidPredicting plasmid contigs from assemblies.
Transmission DynamicsSTARCSResCapRepository for software, raw data tables and data bases.
Transmission DynamicsSTARCSPATOA R package designed to analyze pangenomes (set of genomes) intra or inter species.
Transmission DynamicsSTARCSMetaTORMetagenomic Tridimensional Organisation-based Reassembly – A set of scripts that streamlines the processing and binning of metagenomic metaHiC datasets.
Transmission DynamicsSpARKPathogen Watch databaseGenome reference data for Klebsiella genus.
Transmission DynamicsSpARKmSWEEP softwareFast and accurate bacterial community composition estimation on strain level by using pseudoalignments and variational inference.
Transmission DynamicsST131TSBioinformatic freetware-AccNETA comparative genomic tool for accessory genome analysis using bipartite networks.
Transmission DynamicsST131TSPATOPangenome Analysis Toolkit
Transmission DynamicsPREPAREinferenceFitnessLandscapeStatistical method for fitness landscape inference from experimental evolution data
Transmission DynamicsPREPAREempiricISTStatistical method for analysis of deep mutational scanning fitness data
Transmission DynamicsMACOTRABlast taxon resolverNovel algorithm and software to improve precision of DNA metabarcoding in microbiota analyses
Transmission DynamicsMACOTRAstrain_growthDehydration model
Transmission DynamicsMACOTRAMACOTRA strain collection metadata databaseMACOTRA strain collection metadata database
Transmission DynamicsJumpARSMART databaseThe MGE recombinase sequence models (HMMs) generated in this study are available for public access with SMART database.
Transmission DynamicsJumpARNeighborsScanComputational pipeline for functional annotation of MGErelated tyrosine recombinases.
Transmission DynamicsHECTORNCBI BioProjectWhole-genome sequencing data of 1198 strains, together with metadata.