jlumpe / gambitLinks
A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
☆35Updated 7 months ago
Alternatives and similar repositories for gambit
Users that are interested in gambit are comparing it to the libraries listed below
Sorting:
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 3 months ago
- Library of sketching functions used by PopPUNK☆31Updated 3 months ago
- Genome size estimation from long read overlaps☆58Updated last week
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆36Updated 3 months ago
- In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data☆19Updated last year
- Recombination-free trees☆58Updated 3 months ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 4 months ago
- UPHL's Reference Free Pipeline☆26Updated 2 weeks ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated 2 months ago
- Plasmid analysis using rearrangement distances☆42Updated last month
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated this week
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated last month
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆25Updated 3 weeks ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 2 months ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆36Updated last year
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆22Updated this week
- Rapid discovery of novel prophages using biological feature engineering and machine learning☆37Updated 6 months ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆39Updated last week
- Microbial agile accurate SNP Typer☆30Updated last year
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated 9 months ago
- Strain Resolution ON Graphs☆48Updated last year
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆31Updated 3 months ago
- Colinear block visualisation tool☆31Updated last year
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- Intra-species bacterial contamination detection☆25Updated 5 months ago
- mGEMS Genomic epidemiology with mixed samples☆16Updated 10 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆46Updated this week
- A new high-resolution long-read metagenome assembler for even noisy reads☆74Updated last month
- Bifrost graph gene caller.☆95Updated 9 months ago