rrwick / VerticallLinks
Recombination-free trees
☆59Updated 5 months ago
Alternatives and similar repositories for Verticall
Users that are interested in Verticall are comparing it to the libraries listed below
Sorting:
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆60Updated 2 months ago
- Split Kmer Analysis☆65Updated 3 years ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆41Updated 5 months ago
- Calculate assocations between genes and traits☆25Updated 5 months ago
- reference-based long read assemblies of bacterial genomes☆50Updated 4 years ago
- A tool for removing redundant genomes from a set of assemblies☆76Updated 2 years ago
- Bacterial GWAS analysis☆43Updated last month
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆30Updated 10 months ago
- Split k-mer analysis – version 2☆88Updated last month
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆43Updated 2 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆49Updated last month
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- post processing of bacterial pangenome gene presence/absence matrices☆60Updated 6 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆38Updated 2 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated this week
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆49Updated 2 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆36Updated 4 months ago
- Bifrost graph gene caller.☆96Updated 11 months ago
- A toolkit for prokaryotic comparative genomics☆50Updated 7 months ago
- Intra-species bacterial contamination detection☆25Updated 6 months ago
- Identify phage regions in bacterial genomes for masking purposes☆34Updated 5 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆53Updated 4 months ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Updated 3 years ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆31Updated last month
- Order and orientation of complete bacterial genomes☆28Updated last month
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago