amkram / shusher
Private, browser-based placement of genome sequences on phylogenetic trees using UShER.
☆10Updated 5 months ago
Alternatives and similar repositories for shusher:
Users that are interested in shusher are comparing it to the libraries listed below
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated last week
- ☆14Updated 3 weeks ago
- Genome size estimation from long read overlaps☆52Updated last week
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated 2 weeks ago
- ☆20Updated last month
- ☆9Updated 2 years ago
- Methods to determine sequence element (unitig) presence/absence☆20Updated 4 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Updated last year
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆32Updated last year
- Variant call verification☆16Updated 3 months ago
- A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.☆10Updated this week
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…☆17Updated 2 years ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated last year
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆29Updated 3 weeks ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 2 weeks ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- software to identify primers that can distinguish genomes☆21Updated 3 months ago
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆22Updated last week
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆37Updated last month
- A pipeline for bioinformatics analysis of bacterial genomes☆22Updated 3 weeks ago
- ☆11Updated 2 years ago
- Computation of average nucleotide identity with the use of MMseqs2☆13Updated 4 months ago
- Python implementation of barrnap (Bacterial ribosomal RNA predictor)☆17Updated 3 months ago
- Visualize microbial evolution at the SNP level!☆14Updated 5 months ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆23Updated last year
- ☆17Updated 10 months ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆37Updated 2 weeks ago
- Drug Resistance Prediction with Reference Graphs☆20Updated last year
- viralFlye pipeline☆18Updated 8 months ago