jonas-fuchs / virHEAT
Visualize microbial evolution at the SNP level!
☆13Updated last week
Related projects ⓘ
Alternatives and complementary repositories for virHEAT
- 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 6 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- Finding regions of similarity between plasmids☆16Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆41Updated 4 months ago
- software to identify primers that can distinguish genomes☆20Updated 2 weeks ago
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 4 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 7 months ago
- Targeted Detection and Reconstruction of Plasmids☆19Updated 6 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated this week
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆16Updated this week
- Plasmid analysis using rearrangement distances☆30Updated last week
- CFSAN Shigella Typing Pipeline☆14Updated last year
- MetagenOmic read Re-Assigner and abundance quantifier☆18Updated 5 months ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆11Updated last year
- NCBI Pathogen Detection Portal toolkit☆11Updated last year
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- µbinfie blog☆16Updated 3 weeks ago
- Organism-specific interpretation of AMR genotypes☆9Updated 8 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆40Updated 3 weeks ago
- ccfind - circular complete genome finder with clues of terminal redundancy☆15Updated 4 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆21Updated last year
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated this week
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆20Updated 8 months ago
- Code to create a PRG from a Multiple Sequence Alignment file☆22Updated 7 months ago
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆9Updated 3 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆22Updated last month
- In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data☆19Updated 6 months ago
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆11Updated 7 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 4 months ago