The snakyVC pipeline is designed for efficiently and parallelly executing variant calling on next-generation sequencing (NGS) whole-genome datasets.
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Jun 3, 2025 - Python
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bwa
Here are 15 public repositories matching this topic...
Small GATK alignment and variant calling pipeline using python
pipeline genomics parallel vcf python-wrapper alignment population population-genomics variant-calling bwa bwa-mem gatk4
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Jul 18, 2022 - Python
The second part of https://github.com/npanuhin/BIOCAD
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Mar 12, 2021 - Python
A Snakemake pipeline for copy number variant calling without normal tissue samples
bioinformatics snakemake conda cnv bwa panels cna mutect2 targeted-sequencing sequencing-data cnvkit copynumbervariation purecn
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Jul 31, 2025 - Python
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Jun 22, 2017 - Python
Germline variant calling pipeline
bioinformatics snakemake python3 variants variant-calling bwa germline clinical-research varscan pindel vardict germline-variants deepvariant vusion haplotypecaller
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Aug 27, 2025 - Python
Complete pipeline that mirrors the manuscript: reference based assembly with depth masking, de novo checks, phylogeny with configurable models including ModelFinder, and targeted mutation analysis for G and F versus NC_038235.1 and NC_001781.1. Includes CI and environment files for easy setup.
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Sep 30, 2025 - Python
Parse pileup files, generate consensus fasta and calculate heteroplasmy per nucleotide
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Jul 26, 2019 - Python
💧 Automate message sending with Ngl, delivering one message per second for efficient communication and education purposes.
javascript python angular material-design responsive css-animations carousel molecular-graphics flex-layout sidenav sdf fastq haskell-language scroll-events samtools bwa spammer-ngl neural-reconstruction
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Nov 11, 2025 - Python
Scalable and High Performance Variant Calling on Cluster Environments
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Feb 13, 2022 - Python
Map and post-process your bams for SNP calling
reproducible-research bioinformatics-pipeline multiqc bwa whole-exome-sequencing snakemake-workflows fastqc gatk4
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Mar 10, 2021 - Python
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Jul 30, 2020 - Python
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Feb 29, 2024 - Python
The DKFZ alignment workflow plugin originally developed at the eilslabs
workflow bam-files quality-control alignment wes wgbs bwa bwa-mem conda-environment fastq-files roddy
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Oct 5, 2023 - Python
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