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142 repositories
- Demultiplexing pipeline for sequencing data
tools
Publicgenomeqc
PublicCompare the quality of multiple genomes, along with their annotations.scdownstream
PublicA single cell transcriptomics pipeline for QC, integration and making the data presentablemag
PublicAssembly and binning of metagenomesvariantbenchmarking
Publicpixelator
PublicPipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)createtaxdb
PublicParallelised and automated construction of metagenomic classifier databases of different toolssarek
PublicAnalysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencingcrisprseq
PublicA 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`).raredisease
PublicCall and score variants from WGS/WES of rare disease patients.- A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered
tbanalyzer
PublicAn nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.methylseq
PublicMethylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel- Pipeline for testing drug response prediction models in a statistically and biologically sound way.
molkart
PublicA pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)proteinfold
PublicProtein 3D structure prediction pipeline- A single-cell RNAseq pipeline for 10X genomics data
configs
PublicConfig files used to define parameters specific to compute environments at different Institutions