snipit: summarise snps relative to your reference sequence
☆167Jan 13, 2026Updated last month
Alternatives and similar repositories for snipit
Users that are interested in snipit are comparing it to the libraries listed below
Sorting:
- app to collapse Pango lineages for reporting☆13Dec 9, 2025Updated 3 months ago
- Systematic ProtEin AnnotatoR☆19Sep 20, 2025Updated 5 months ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆153Oct 2, 2025Updated 5 months ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆39Feb 20, 2026Updated 2 weeks ago
- SARS-Cov-2 Recombinant Finder for fasta sequences☆50Jun 22, 2022Updated 3 years ago
- Rapid determination of appropriate reference genomes.☆100Jan 22, 2025Updated last year
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆62Updated this week
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆250Feb 25, 2026Updated last week
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation☆114Updated this week
- ☆12Feb 15, 2023Updated 3 years ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Apr 5, 2024Updated last year
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments☆108Dec 11, 2023Updated 2 years ago
- ☆74Jan 23, 2024Updated 2 years ago
- A tool for exploring large trees in the browser☆123Updated this week
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆251Feb 27, 2026Updated last week
- Synteny and Rearrangement Identifier☆448Apr 29, 2025Updated 10 months ago
- Create a tree using Mash distances☆184Oct 24, 2023Updated 2 years ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 3 months ago
- Reorients assembled microbial sequences☆135Aug 21, 2025Updated 6 months ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆13Jun 30, 2023Updated 2 years ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last week
- An updated pipeline for pangenome investigation☆345Jan 15, 2026Updated last month
- Tool to plot synteny and structural rearrangements between genomes☆343Apr 7, 2025Updated 11 months ago
- Ultrafast Sample Placement on Existing Trees☆139Feb 6, 2026Updated last month
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated last month
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆52Jul 24, 2025Updated 7 months ago
- REcombination BARcode detector.☆16Apr 2, 2024Updated last year
- GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…☆87Dec 15, 2024Updated last year
- A toolbox for pangenome analysis and threshold evaluation.☆99Jul 8, 2022Updated 3 years ago
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Aug 5, 2022Updated 3 years ago
- Antibiotic resistance prediction in minutes☆113Nov 24, 2024Updated last year
- 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
- Cluster Investigation & Virus Epidemiology Tool☆50Jun 17, 2025Updated 8 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆220Feb 23, 2026Updated last week
- Split k-mer analysis – version 2☆104Jan 29, 2026Updated last month
- Generate mutated sequence files from a reference genome.☆11Dec 26, 2022Updated 3 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year