A pipeline for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms.

Identification of gene-fusions, including EML4-ALK

Tumor in normal detection

Source code to support the paper: "Extensive mitochondrial population structure and haplotype-specific variation in metabolic phenotypes in the Drosophila Genetic Reference Panel"

A pipeline for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms.

INDELfindR is an command line tool for detecting complex insertions and deletions (indels) from indexed BAM files.

A pipeline to study intratumor heterogeneity (ITH) with Canopy

Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools

Obtaining case-associated variants and correspondent genes (from control/case experiments) in BASH/R enviroment

This repository contains scripts used to collect and analyze data from whole genome sequences of clinical Streptococcus agalactiae (Group B Strep) isolates for the project described in the following manuscript: Pell, M.E. et al., bioRxiv, 2024-04-01.

Pipeline in place at the UGI for DNA level analysis

This repository contains bash shell scripts

NanoSwe: Analysing nanopore (PromethION) data of Swedish genomes

A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.

BSA-QTL Mapping in Drosophila Ananassae

A repository for efficient population genomic analysis using Snakemake workflow.

interactive variant tables for easy filtering

A simple tool for SNP mutation type determination.

Pipelines/Wrappers for evaluating the performance of variant callers on tumor/normal RNA-Seq data

Management flow using PBS system to analyze sequencing data from Illumina Novaseq6000