gtonkinhill / tracsLinks
Fast pairwise transmission inference from single genome and/or metagenomic data
☆22Updated 3 months ago
Alternatives and similar repositories for tracs
Users that are interested in tracs are comparing it to the libraries listed below
Sorting:
- Strain-level haplotyping for metagenomes with short or long-reads.☆56Updated 7 months ago
- Plasmid analysis using rearrangement distances☆46Updated 2 months ago
- ☆23Updated this week
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 6 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆19Updated 2 years ago
- ☆24Updated 9 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Updated 3 years ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated last year
- Calculate assocations between genes and traits☆29Updated 8 months ago
- Automated strain separation of low-complexity metagenomes☆53Updated 4 years ago
- Microbial agile accurate SNP Typer☆29Updated last year
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆31Updated 3 months ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Updated 3 years ago
- viralFlye pipeline☆18Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Recombination-free trees☆60Updated 2 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- Genome size estimation from long read overlaps☆72Updated last week
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆31Updated last week
- Population analysis PIPEline 🛠🧬☆22Updated 6 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 5 months ago
- Unleash the full power of your k-mers!☆24Updated this week
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆51Updated 2 months ago
- A new high-resolution long-read metagenome assembler for even noisy reads☆104Updated 2 months ago
- Downstream processing of VAMB binning for Viral Elucidation☆51Updated last year
- Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes☆11Updated last year
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Updated 8 months ago