jmcbroome / autolin
Repository containing a method for automatically identifying pathogen lineages from a phylogeny.
☆14Updated last year
Related projects ⓘ
Alternatives and complementary repositories for autolin
- ☆13Updated last year
- Methods to determine sequence element (unitig) presence/absence☆18Updated 9 months ago
- Fast, scalable, accurate and accessible Bayesian phylogenetics☆25Updated last week
- Plasmid analysis using rearrangement distances☆29Updated 2 months ago
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12Updated 5 months ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆23Updated last week
- Code to create a PRG from a Multiple Sequence Alignment file☆22Updated 7 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Updated last year
- Non-redundant pangenome assemblies from multiple genomes or bins☆13Updated 3 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆40Updated 4 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- software to identify primers that can distinguish genomes☆20Updated last week
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated 2 months ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆22Updated 6 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆28Updated 2 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- MetagenOmic read Re-Assigner and abundance quantifier☆17Updated 4 months ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆36Updated 10 months ago
- Neptune: Genomic Signature Discovery☆18Updated last week
- ☆19Updated 4 months ago
- A novel method for sequence similarity estimation☆26Updated 7 months ago
- Summarise nucleotide counts at a set of positions in a BAM file to search for mixtures☆13Updated 2 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆20Updated last year
- Manipulate and generate figures for trees in Newick format☆19Updated last year
- Fast viral consensus genome reconstruction☆22Updated 4 months ago
- Scaffolding with assembly likelihood optimization☆20Updated 3 years ago
- ☆17Updated 5 months ago
- A pipeline for whole genome assembly☆16Updated 2 years ago
- Intra-species bacterial contamination detection☆22Updated last year
- Variant call verification☆15Updated last year