bvalot / pyMLSTLinks
whole genome MLST analysis
☆50Updated 6 months ago
Alternatives and similar repositories for pyMLST
Users that are interested in pyMLST are comparing it to the libraries listed below
Sorting:
- post processing of bacterial pangenome gene presence/absence matrices☆63Updated 9 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Updated 4 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆32Updated last week
- Bacterial GWAS analysis☆46Updated last month
- GTDB taxonomy taxdump files with trackable TaxIds☆56Updated 7 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
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆62Updated 2 years ago
- A toolkit for prokaryotic comparative genomics☆51Updated last month
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆41Updated 4 years ago
- A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.☆50Updated 3 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 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 surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆47Updated last month
- Calculate assocations between genes and traits☆29Updated 9 months ago
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 months ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆44Updated 4 months ago
- Identify phage regions in bacterial genomes for masking purposes☆34Updated 6 years ago
- Bifrost graph gene caller.☆96Updated 2 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 5 months ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆70Updated 3 weeks ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆46Updated 2 years ago
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆49Updated 2 years ago
- Graph-based assembly phasing☆90Updated 2 weeks ago
- ☆20Updated last year
- Gene Absence Presence Identification tool.☆27Updated 8 months ago
- ☆54Updated 5 months ago
- A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing☆51Updated 2 weeks ago
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆55Updated last month
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- Split Kmer Analysis☆66Updated 3 years ago