Private, browser-based placement of genome sequences on phylogenetic trees using UShER.
☆11Nov 22, 2024Updated last year
Alternatives and similar repositories for shusher
Users that are interested in shusher are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Cython API for the Mutation Annotated Tree (MAT) Online Phylogenetics Toolkit☆14May 28, 2025Updated 9 months ago
- A tool for exploring large trees in the browser☆125Mar 17, 2026Updated last week
- Ultrafast Sample Placement on Existing Trees☆139Feb 6, 2026Updated last month
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36May 1, 2022Updated 3 years ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated 3 weeks ago
- TQSLE v1.0 released☆10Aug 29, 2023Updated 2 years ago
- app to collapse Pango lineages for reporting☆13Dec 9, 2025Updated 3 months ago
- Fast, scalable, accurate and accessible Bayesian phylogenetics☆43Updated this week
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- Summarise nucleotide counts at a set of positions in a BAM file to search for mixtures☆13Apr 5, 2022Updated 3 years ago
- Instantaneous Metagenome Taxonomic Profiling with MetaKSSD☆24Nov 3, 2025Updated 4 months ago
- curPrimers is a tool for trimming primer sequences from amplicon based NGS reads☆17May 26, 2025Updated 9 months ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- SeqWho - A reliable and rapid FASTQ(A) file classifier☆10Jan 21, 2022Updated 4 years ago
- ☆32Jan 5, 2023Updated 3 years ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- ☆18Dec 26, 2025Updated 2 months ago
- Sketch-based surveillance platform☆14Dec 17, 2024Updated last year
- Estimating time trees from very large phylogenies☆28Jul 21, 2024Updated last year
- Pipeline for analyzing rare mutations in metagenome-assembled genomes☆10Apr 4, 2025Updated 11 months ago
- Hybrid Assembler for Plasmids☆10Jul 28, 2022Updated 3 years ago
- Sketch phylogenetic trees and networks☆24Feb 5, 2026Updated last month
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 2 years ago
- Ultra-rapid detection of viral variants directly from sequencing data☆38Feb 17, 2026Updated last month
- Computation of average nucleotide identity with the use of MMseqs2☆16Dec 11, 2024Updated last year
- ☆17Aug 11, 2025Updated 7 months ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- Simulation of Epistasis Local adaptation, with Ancestry and Mate choice☆11Apr 22, 2023Updated 2 years ago
- emm Automatic Isolate Labeller☆12Mar 25, 2025Updated last year
- A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.☆21Mar 13, 2026Updated last week
- REcombination BARcode detector.☆16Apr 2, 2024Updated last year
- de Bruijn graph cOrrectiOn from graph aLignment☆11Jul 20, 2020Updated 5 years ago
- Population analysis PIPEline 🛠🧬☆23Mar 2, 2026Updated 3 weeks ago
- Banded Striped DNA Sequence Alignment☆52May 9, 2023Updated 2 years ago
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.☆16Updated this week
- Python Toolkit for using containerized programs in either Singularity or Docker☆29Mar 19, 2024Updated 2 years ago
- Global phylogenies of SARS-CoV-2 sequences☆85Oct 24, 2023Updated 2 years ago
- Assembly of Nanopore Sequencing☆17Jan 8, 2026Updated 2 months ago
- This is the GPress, a framework for querying GTF, GFF3 and expression files in a compressed form.☆11Oct 5, 2023Updated 2 years ago