Simple ChIP-seq simulation data generator.

NGS analysis pipeline for ATAC-seq experiments.

Implementation of the Analytic Hierarchy Process (AHP) to obtain the immunogenicity score of wheat lines based on their celiac disease (CD) epitopes matches on alpha- and gamma-gliadins amplicons by NGS and the score for oligopeptides based on an IFN-g ELISpot assays with fresh peripherical blood mononuclear cells (PBMCs).

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data

Pooling Illumina NextSeq 500 fastq files

Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).

software for processing tuberculosis whole genome data. interface to the BWA, VarScan, SamTools etc.

Micro-libraries for reading and writing genomic sequence data in various formats.

RAD-seq protocols for the Agilent NGS workstation option B.

Repository for pan-spefic primers designed for tiled full genome sequencing or qPCR of viral pathogens. Pathogens include amongst others Hepatitis E virus, Hepatitis A virus, Poliovirus and SARS-COV-2. Primers were designed with varVAMP.

Workflow to perform a Variant Calling Analysis

Notebooks and examples for DeepVariant on Spark project.

Protein Analysis and Classifier Toolkit

Exchange platform for sharing issues and advice during the training

DEmultiplexing MOnitoring Report Tool. DEMORT evaluates demultiplexed fastq files by computing various metrics.

A pipeline utilizing PCA on 1000 genomes and WGS data from your own samples to determine or validate ancestry of an individual.

Code and scripts used for Worth et al. 2022: "Receptor editing constrains development of phosphatidyl choline-specific B cells in VH12-transgenic mice".

A script to report depth of coverage from BAM/SAM/CRAM file or parse the output generated from "samtools depth"

conserved sequenc-based degenerate primer design tool