Small GATK alignment and variant calling pipeline using python
A Snakemake pipeline for copy number variant calling without normal tissue samples
The snakyVC pipeline is designed for efficiently and parallelly executing variant calling on next-generation sequencing (NGS) whole-genome datasets.
The second part of https://github.com/npanuhin/BIOCAD
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.
Germline variant calling pipeline
Parse pileup files, generate consensus fasta and calculate heteroplasmy per nucleotide
Scalable and High Performance Variant Calling on Cluster Environments
💧 Automate message sending with Ngl, delivering one message per second for efficient communication and education purposes.
Map and post-process your bams for SNP calling
The DKFZ alignment workflow plugin originally developed at the eilslabs
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