PiGx SARS-CoV-2 wastewater sequencing pipeline
☆18May 3, 2023Updated 2 years ago
Alternatives and similar repositories for pigx_sars-cov-2
Users that are interested in pigx_sars-cov-2 are comparing it to the libraries listed below
Sorting:
- Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification☆15Sep 27, 2023Updated 2 years ago
- SARS-CoV-2 (Va)riant (Qu)antification in s(E)wage, designed for (Ro)bustness☆13Oct 10, 2025Updated 4 months ago
- ☆19Nov 24, 2025Updated 3 months ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- viral-ngs: complete pipelines☆73Feb 27, 2026Updated last week
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last week
- GitHub Actions for developing and maintaining Bioconductor packages☆13Nov 13, 2025Updated 3 months ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated 2 weeks ago
- command-line and python interface to the uniprot database☆10Jun 11, 2015Updated 10 years ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Jul 13, 2023Updated 2 years ago
- ☆16Aug 8, 2025Updated 7 months ago
- This is a deep learning method for identification of viral contigs with short length from metagenomic data.☆10Dec 20, 2021Updated 4 years ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆13Aug 26, 2024Updated last year
- The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linka…☆13May 23, 2023Updated 2 years ago
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)☆32Feb 7, 2026Updated last month
- ☆27Aug 2, 2023Updated 2 years ago
- ☆30Dec 22, 2023Updated 2 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
- mreps: software for tandem repeat identification in DNA☆15Nov 13, 2019Updated 6 years ago
- a comparative genome browser for bacteriophages☆20Jan 17, 2025Updated last year
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- Variant Alert!, a framework to monitor every significant alteration in variant classification and gene-disease association between two ve…☆14Jul 19, 2021Updated 4 years ago
- A streaming method for mapping nanopore raw signals☆32Nov 7, 2021Updated 4 years ago
- 📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria☆41Oct 28, 2025Updated 4 months ago
- Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash and UltraLogLog☆19Jan 22, 2026Updated last month
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.☆16Updated this week
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- A functional profiler for metagenomes using FracMinHash☆21Jul 14, 2025Updated 7 months ago
- SARS-Cov-2 Recombinant Finder for fasta sequences☆50Jun 22, 2022Updated 3 years ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 3 months ago
- Programmatically interact with the GISAID database.☆80Aug 5, 2025Updated 7 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Jun 26, 2018Updated 7 years ago
- ☆17Nov 19, 2024Updated last year
- Kraken2 Server☆23Nov 24, 2025Updated 3 months ago
- VIGOR4☆21Aug 15, 2025Updated 6 months ago
- syncmer graphs, and perhaps other sorts of sequence graphs☆24Mar 1, 2026Updated last week
- ARTIC SARS-CoV-2 workflow and reporting☆50Apr 25, 2025Updated 10 months ago