Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
☆13Mar 2, 2026Updated last week
Alternatives and similar repositories for jasen
Users that are interested in jasen are comparing it to the libraries listed below
Sorting:
- A nextflow pipeline for analysing expression and splicing in RNA seq data from rare disease patient☆18Mar 2, 2026Updated last week
- Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity☆17Mar 10, 2022Updated 4 years ago
- do some exercise☆14Dec 2, 2025Updated 3 months ago
- ☆19Feb 27, 2026Updated last week
- Bioinformatics with Unix, bash, Make, Python, and parallel☆22Aug 17, 2020Updated 5 years ago
- A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…☆20Oct 4, 2024Updated last year
- Pipeline in place at the UGI for DNA level analysis☆11Aug 29, 2016Updated 9 years ago
- A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.☆31Mar 3, 2026Updated last week
- A nextflow pipeline for calling exome CNVs☆13Feb 24, 2026Updated 2 weeks ago
- Automated ACMG/AMP classification for human variants associated with congenital hearing loss☆11May 14, 2025Updated 9 months ago
- Cool Bioinformatics Scripts☆12May 21, 2024Updated last year
- Python Programming for Biologists☆12Dec 3, 2025Updated 3 months ago
- A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data☆13Updated this week
- Code used to process and analyze structural variants and short tandem repeat variants profiled in 719 deeply sequenced whole genomes as p…☆11Jun 25, 2019Updated 6 years ago
- A tool to examine duplicate read characteristics in a BAM file☆12Dec 8, 2017Updated 8 years ago
- Rails application for storing and parsing clinical exome VCF files. Gene annotations can be retrieved via Biomart integration from Ensemb…☆10May 7, 2017Updated 8 years ago
- MetaPORE – Chiu Laboratory, University of California, San Francisco☆12Nov 4, 2015Updated 10 years ago
- GitHub repository for GenErode, a Snakemake workflow for the analysis of whole-genome sequencing data from historical and modern samples …☆31Feb 27, 2026Updated last week
- This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially …☆27Jul 28, 2025Updated 7 months ago
- Collection of R scripts for SARS-CoV-2 (variant) analyses☆12Mar 2, 2023Updated 3 years ago
- C++ library for parsing several formats in bioinformatics☆10May 18, 2023Updated 2 years ago
- Tutorials for data science and bioinformatics☆13May 3, 2024Updated last year
- Functional code templates for the Star Protocols paper describing consolidated WES variant calling with 3 callers☆10Oct 18, 2024Updated last year
- A nextflow version of the Wochenende reference metagenome binning and visualization pipeline☆15Updated this week
- Pipeline for Illumina shotgun sequencing of 16S rRNA amplicon sequences☆14Sep 2, 2016Updated 9 years ago
- Clin.iobio - Workflow and reporting for iobio variant analysis pipeline☆12Oct 7, 2025Updated 5 months ago
- Curated list of resources for variant prioritization☆14Nov 18, 2025Updated 3 months ago
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 5 years ago
- ☆27Mar 2, 2026Updated last week
- RTG Core: Software for alignment and analysis of next-gen sequencing data.☆49May 27, 2025Updated 9 months ago
- A tool kit to manage many variant on desktop computer☆13Jan 13, 2026Updated last month
- GenomeTools: Scripts and Classes for Working with Genomic Data☆12Jun 7, 2018Updated 7 years ago
- laSV is a software package that employs local assembly to detect structural variations from whole-genome high-throughput sequencing datas…☆12Sep 26, 2016Updated 9 years ago
- Nanopore plasmid pipeline (FAST5 basecalling, assembly, plasmid identification and antimicrobial resistance genes identification).☆13Apr 20, 2021Updated 4 years ago
- Official code repository for JAX-CNV☆14Jan 16, 2020Updated 6 years ago
- This is a deep learning method for identification of viral contigs with short length from metagenomic data.☆10Dec 20, 2021Updated 4 years ago
- Order and orientation of complete bacterial genomes☆29Jul 11, 2025Updated 7 months ago
- A method to improve mappings on circular genomes, using the BWA mapper☆10Mar 4, 2022Updated 4 years ago
- ☆15Nov 28, 2022Updated 3 years ago