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- Assembly and binning of metagenomes
- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
- Call and score variants from WGS/WES of rare disease patients.
modules
Public- Parallelised and automated construction of metagenomic classifier databases of different tools
- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
- Amplicon sequencing analysis workflow using DADA2 and QIIME2
variantbenchmarking
Public- Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
demultiplex
PublicDemultiplexing pipeline for sequencing data- Config files used to define parameters specific to compute environments at different Institutions
oncoanalyser
Public- Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.
pathogensurveillance
Publicdetaxizer
Publicrangeland
PublicPipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.demo
Publiceager
PublicA fully reproducible and state-of-the-art ancient DNA analysis pipeline- circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
- A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
scrnaseq
PublicA single-cell RNAseq pipeline for 10X genomics data