insapathogenomics / ReporTreeLinks
A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
☆47Updated 2 months ago
Alternatives and similar repositories for ReporTree
Users that are interested in ReporTree are comparing it to the libraries listed below
Sorting:
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Updated 4 years ago
- Split Kmer Analysis☆66Updated 3 years ago
- Identify phage regions in bacterial genomes for masking purposes☆34Updated 6 years ago
- Recombination-free trees☆64Updated 3 months ago
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆48Updated last week
- Bacterial GWAS analysis☆46Updated last month
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆55Updated 2 months ago
- A toolkit for prokaryotic comparative genomics☆51Updated 2 months ago
- a collection of scripts for organising bacterial genomes by species☆81Updated 3 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Calculate assocations between genes and traits☆29Updated 9 months ago
- Bifrost graph gene caller.☆96Updated 3 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆70Updated this week
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 6 months ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- Predict plasmids from uncorrected long read data☆41Updated last month
- Gene-flank analysis tool☆34Updated last year
- PLSDB pipeline to collect bacterial plasmids from NCBI☆39Updated last year
- GTDB taxonomy taxdump files with trackable TaxIds☆56Updated 7 months ago
- whole genome MLST analysis☆50Updated 6 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Updated 5 years ago
- Discover and annotate the virome☆56Updated 2 months ago
- post processing of bacterial pangenome gene presence/absence matrices☆63Updated 10 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆60Updated last week
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago