metalhelix / pipetteView external linksLinks
variant discovery and annotation using GATK and Ensembl
☆17Jun 27, 2013Updated 12 years ago
Alternatives and similar repositories for pipette
Users that are interested in pipette are comparing it to the libraries listed below
Sorting:
- Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data☆33Oct 25, 2013Updated 12 years ago
- Directly create a bigwig file with signal derived from a sorted and indexed bam file.☆11Jul 7, 2017Updated 8 years ago
- Alignment and variant-calling pipeline for Illumina HIV sequences.☆11May 19, 2020Updated 5 years ago
- Set of tools for viral metagenomics.☆14Jan 21, 2026Updated 3 weeks ago
- Strain resolved metagenome simulator☆13Aug 11, 2018Updated 7 years ago
- Please see https://github.com/chanzuckerberg/czid-workflows for the latest version of CZ ID workflows.☆27Jan 10, 2022Updated 4 years ago
- vcf file manipulation☆22Jul 9, 2015Updated 10 years ago
- Trigger the Google Genomics Pipeline API with CWL☆11Feb 7, 2017Updated 9 years ago
- robust matching of small variant datasets using flexible scoring schemes☆11Mar 26, 2020Updated 5 years ago
- R tools to interact with hap.py output☆16Jul 12, 2019Updated 6 years ago
- A simple variant calling and annotation pipeline using BWA, GATK and ENSEMBL.☆14Nov 29, 2013Updated 12 years ago
- RNAsik - more than just a pipeline☆13Feb 6, 2024Updated 2 years ago
- Generate and process BAM files from Illumina sequencing instrument files☆23Feb 25, 2016Updated 9 years ago
- A configurable de novo assembly pipeline☆28Jun 29, 2016Updated 9 years ago
- Visualization and charting JS library for streaming genomic data☆19Dec 4, 2024Updated last year
- Convert CWL to WDL☆17Oct 17, 2016Updated 9 years ago
- Probabilistic inference of viral quasispecies subject to recombination (viral haplotype reconstruction).☆20May 3, 2017Updated 8 years ago
- Job Manager API and UI for interacting with asynchronous batch jobs and workflows.☆27Feb 6, 2026Updated last week
- Community-maintained list of resources that the CI4CC organization and the larger cancer informatics community have found useful or are d…☆22Sep 24, 2018Updated 7 years ago
- Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang☆47Jul 12, 2020Updated 5 years ago
- BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants☆25Mar 17, 2016Updated 9 years ago
- Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities☆25Oct 31, 2019Updated 6 years ago
- LoFreq Version 3☆27Feb 25, 2021Updated 4 years ago
- ☆22Feb 7, 2020Updated 6 years ago
- ALPACA is a caller for genomic variants (single nucleotide and small indels) from next-generation sequencing data that uses a novel algeb…☆23Nov 19, 2024Updated last year
- paplot creates various dynamic and interactive reports for cancer genome analysis.☆26Feb 1, 2023Updated 3 years ago
- A COVID-19 CoV Genetics (CG) browser to inform therapeutics development☆26Jan 12, 2026Updated last month
- [Experimental] Workflow Definition Language (WDL) to CWL☆28Nov 17, 2021Updated 4 years ago
- 📊Evaluating, filtering, comparing, and visualising VCF☆28Mar 9, 2023Updated 2 years ago
- List of computational resources for analyzing microbial sequencing data.☆67Nov 18, 2025Updated 2 months ago
- CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.☆30Feb 20, 2021Updated 4 years ago
- Phylogenetic placement and downstream analysis☆89Jan 28, 2026Updated 2 weeks ago
- ☆28Oct 5, 2018Updated 7 years ago
- Remove primer sequence from BAM alignments by soft-clipping☆31Dec 5, 2019Updated 6 years ago
- Add biological annotations to variants in a given VCF file.☆32Sep 13, 2021Updated 4 years ago
- The Genome U-Plot is a JavaScript tool to visualize chromosomal abnormalities in the Human Genome using a U-shape layout.☆32Dec 10, 2022Updated 3 years ago
- Simplify snpEff annotations for interesting cases☆22Feb 18, 2019Updated 6 years ago
- BigWig manpulation tools using libBigWig and htslib☆30Aug 8, 2024Updated last year
- viral-ngs: command line tools and wrappers for processing raw viral genomic data☆193Updated this week