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bioinformatics-algo-labs

cancer_genomics

Repository for lectures

expression-quantification

A BioWDL workflow for quantifying expression. Category:Multi-Sample

gatk-preprocess

A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. Category:Single-Sample

gatk4-data-processing

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

gatk4-mitochondria-pipeline

This repo is be archived, these workflows are still housed housed in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

gatk4-pathseq

This repo is archived, the these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

gatk4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

mouse-go-analysis

This repository represents a bioinformatic pipeline to carry Gene Ontology analysis for high divergence genes used as an exercise at the course on Unix and work with genomic data

prirodou-inspirovane-algoritmy

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data