interactive barplot for amplicon sequencing
☆13Dec 5, 2024Updated last year
Alternatives and similar repositories for amplicon_coverage_plot
Users that are interested in amplicon_coverage_plot are comparing it to the libraries listed below
Sorting:
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated 3 weeks ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Sketch-based surveillance platform☆14Dec 17, 2024Updated last year
- FluMut is a command-line tool to find markers of interest in H5N1 avian influenza viruses.☆13Feb 3, 2026Updated last month
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- UPHL's Reference Free Pipeline☆27Updated this week
- Static website for the PH4AGE alliance☆13Oct 27, 2023Updated 2 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆38Jan 22, 2026Updated last month
- Biological file format specimens for testing packages, and functions to assist in testing.☆15Nov 18, 2025Updated 4 months ago
- VIGOR4☆21Aug 15, 2025Updated 7 months ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing libra…☆15Feb 27, 2024Updated 2 years ago
- Remove primer sequence from BAM alignments by soft-clipping☆30Dec 5, 2019Updated 6 years ago
- Rapid determination of appropriate reference genomes.☆100Jan 22, 2025Updated last year
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated last month
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 4 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 8 months ago
- Plasmid and antimicrobial resistance pipeline☆16Dec 30, 2024Updated last year
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 5 years ago
- Antimicrobial Resistance Analysis☆10Jun 11, 2024Updated last year
- Fasten toolkit, for streaming operations on fastq files☆81Oct 24, 2025Updated 4 months ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 4 months ago
- ☆74Jan 23, 2024Updated 2 years ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆13Jun 30, 2023Updated 2 years ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 5 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Jul 2, 2024Updated last year
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated last month
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Sep 22, 2022Updated 3 years ago
- The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized f…☆14Apr 21, 2023Updated 2 years ago
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆20Nov 24, 2024Updated last year
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆18Updated this week
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆28Mar 10, 2026Updated last week
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆170Mar 22, 2023Updated 2 years ago
- Add biological annotations to variants in a given VCF file.☆32Sep 13, 2021Updated 4 years ago
- Full-length de novo viral haplotype reconstruction from noisy long reads☆21Nov 6, 2023Updated 2 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆63Updated this week
- Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.☆144Mar 13, 2026Updated last week