Docker containers for bioinformatics with a small footprint
☆23Dec 18, 2025Updated 2 months ago
Alternatives and similar repositories for kogia
Users that are interested in kogia are comparing it to the libraries listed below
Sorting:
- k-mer similarity analysis pipeline☆21Nov 20, 2025Updated 3 months ago
- Viral genome coverage evaluation for metagenomic diagnostics☆27Aug 19, 2025Updated 6 months ago
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- IndexTools is a toolkit for extremely fast NGS analysis based on index files.☆17Aug 19, 2022Updated 3 years ago
- Nextflow language support for Visual Studio Editor☆37Feb 27, 2026Updated last week
- UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies☆27May 13, 2025Updated 9 months ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Feb 20, 2026Updated 2 weeks ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- PipeTaxon exposes the ncbi taxonomy database as a REST API.☆22Feb 15, 2023Updated 3 years ago
- Reference Phylogeny for Bacterial and Archaeal Genomes☆25Aug 9, 2025Updated 6 months ago
- Python CLI for alignment-free genomics.☆13Feb 11, 2026Updated 3 weeks ago
- A Nextflow pipeline to play Doom☆10Dec 1, 2025Updated 3 months ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last week
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- Finding cryptic relationships to boost disease gene detection☆12May 31, 2023Updated 2 years ago
- GraphSNP: Using graph approach to investigate outbreak cluster and transmission in a web browser☆12Oct 5, 2025Updated 5 months ago
- Ploidy agnostic phasing pipeline and algorithm☆49Jan 3, 2024Updated 2 years ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated 2 weeks ago
- taxonomic classifier based on the kraken2 algorithms and more☆46Dec 12, 2025Updated 2 months ago
- Python implementation and field-tool for automated pipeline launching through Tower CLI (beta)☆33Dec 1, 2025Updated 3 months ago
- A library for manipulating bioinformatics sequencing formats in Apache Spark☆32Updated this week
- Unsupervised Clustering of Environmental Microbial Assemblies Using Coverage and Affinity Propagation☆31May 25, 2021Updated 4 years ago
- Antibiotic resistance prediction in minutes☆113Nov 24, 2024Updated last year
- Bioinformatics pipeline to identify differentially active transcription factors between conditions using expression and epigenetic data☆14Mar 12, 2024Updated last year
- A curated database of completed assemblies with taxonomy IDs☆51Feb 25, 2026Updated last week
- Search for a set of compatible indexes for your sequencing experiment☆11Sep 6, 2019Updated 6 years ago
- convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region☆13May 21, 2024Updated last year
- A collaborative notebook for genes and genomes☆13Feb 12, 2026Updated 3 weeks ago
- 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
- A server for maintaining high-throughput sequencing QC data☆13Aug 5, 2025Updated 7 months ago
- nf-core/references is a bioinformatics pipeline that build references, for multiple use cases☆19Jan 15, 2026Updated last month
- A Python interface to the Ensembl REST APIs, biological data at your fingertips.☆11Apr 17, 2024Updated last year
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆63Updated this week
- ☆29Jun 12, 2024Updated last year
- ☆27Aug 2, 2023Updated 2 years ago
- Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.☆32Nov 19, 2025Updated 3 months ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year