The Wayback Machine - https://web.archive.org/web/20211104125656/https://github.com/topics/variant-calling
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161 public repositories
matching this topic...
Python library to facilitate genome assembly, annotation, and comparative genomics
Updated
Nov 4, 2021
Python
C++ library and cmdline tools for parsing and manipulating VCF files
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Bayesian haplotype-based mutation calling
A tool set for short variant discovery in genetic sequence data.
Viral genomics analysis pipelines
Updated
Nov 3, 2020
Python
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Updated
Nov 4, 2020
Python
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Updated
Nov 3, 2021
Nextflow
PEPPER-Margin-DeepVariant
Updated
Nov 3, 2021
Python
Fast and accurate gene fusion detection from RNA-Seq data
Sequana: a set of Snakemake NGS pipelines
Updated
Nov 3, 2021
Jupyter Notebook
Graph realignment tools for structural variants
De novo genome assembly and multisample variant calling
PacBio® variant and consensus caller
Updated
Apr 25, 2019
Python
De novo assembly based variant calling pipeline for Illumina short reads
💾 📃 "Reads to report" for public health and clinical microbiology
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
Updated
May 17, 2021
Python
GATK RNA-Seq Variant Calling in Nextflow
Updated
Aug 25, 2021
Nextflow
Genome inference from a population reference graph
CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
xHLA: Fast and accurate HLA typing from short read sequence data
Updated
Oct 11, 2018
Jupyter Notebook
A method for variant graph genotyping based on exact alignment of k-mers
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.
A tool for fast and accurate summarizing of variant calling format (VCF) files
Updated
Sep 9, 2021
Python
Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
Clair3 - Integrating pileup and full-alignment for high-performance long-read variant calling
Updated
Oct 25, 2021
Python
Assembly and intrahost/low-frequency variant calling for viral samples
Updated
Jul 29, 2021
Nextflow
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Hi there,
Thanks for writing such an excellent piece of software. The pace of development has definitely outstripped the updates in documentation--and as a newbie to ONT analysis, I was hoping that I could point out some of the pain points and help improve docs for others in my shoes.
The doc that I depended the most on was https://nanoporetech.github.io/megalodon/file_formats.html.
**Lin