esteinig / sketchyLinks
Genomic neighbor typing of bacterial pathogens using MinHash
☆43Updated 2 years ago
Alternatives and similar repositories for sketchy
Users that are interested in sketchy are comparing it to the libraries listed below
Sorting:
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆31Updated 2 weeks ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 5 months ago
- software to identify primers that can distinguish genomes☆20Updated 7 months ago
- Genome size estimation from long read overlaps☆61Updated 3 weeks ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated last week
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 6 months ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 weeks ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Colinear block visualisation tool☆31Updated last year
- Automated strain separation of low-complexity metagenomes☆50Updated 3 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆45Updated 2 months ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Updated 2 years ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆37Updated last year
- Remove human reads from a sequencing run☆40Updated last month
- Intra-species bacterial contamination detection☆25Updated 7 months ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆46Updated 2 years ago
- In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data☆20Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆27Updated 2 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated last week
- Recombination-free trees☆60Updated 3 weeks ago
- reference-based long read assemblies of bacterial genomes☆50Updated 4 years ago
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- ☆14Updated 4 years ago
- Read contamination removal☆25Updated last year
- Library of sketching functions used by PopPUNK☆30Updated 5 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 6 years ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆26Updated last month