philarevalo / PopCOGenTLinks
Microbial Populations as Clusters Of Gene Transfer
☆44Updated last year
Alternatives and similar repositories for PopCOGenT
Users that are interested in PopCOGenT are comparing it to the libraries listed below
Sorting:
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆43Updated 2 years ago
- A toolbox for improving metagenome-assembled genomes.☆63Updated 4 years ago
- A tool for removing redundant genomes from a set of assemblies☆76Updated 2 years ago
- post processing of bacterial pangenome gene presence/absence matrices☆60Updated 6 months ago
- Ley Lab MetaGenome Profiler DataBase generator☆50Updated 2 years ago
- GTDB taxonomy taxdump files with trackable TaxIds☆56Updated 4 months ago
- ☆53Updated last month
- Horizontal gene transfer (HGT) identification pipeline☆63Updated 2 years ago
- ☆25Updated 6 years ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆22Updated 2 years ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆61Updated last year
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 4 years ago
- whole genome MLST analysis☆46Updated 2 months ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆34Updated 2 years ago
- Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…☆59Updated 4 months ago
- Tool to estimate genome quality of microbial eukaryotes☆38Updated 3 weeks ago
- IslandPath standalone software☆33Updated last year
- EzAAI - High Throughput Prokaryotic AAI Calculator☆44Updated 3 weeks ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆73Updated 5 years ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆62Updated 3 weeks ago
- A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concat…☆59Updated 7 months ago
- Improvement of metagenome-assembled genomes☆54Updated 5 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Updated last year
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆30Updated 10 months ago
- tiara – a tool for DNA sequence classification☆66Updated last year
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆42Updated 4 years ago
- Gene Absence Presence Identification tool.☆27Updated 5 months ago
- A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing☆49Updated 2 months ago
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆74Updated last year