Jakob Schuster

alpseq is an open-source pipeline for processing NGS data from nanobody libraries, enabling efficient analysis and identification of enriched sequences.

matchbox provides a flexible and scalable read processor for handling diverse sequencing tasks, demonstrating versatility in demultiplexing, restranding, CRISPR efficiency assessment, and haplotyping.

FLAMESv2 is a flexible R/Bioconductor package for analyzing long-read single-cell RNA-seq data, demonstrating field-leading performance in isoform analysis and cell-type identification.

Restrander improves the orientation and quality control of long-read cDNA data by accurately inferring strandedness and detecting artefacts.

The paper develops FLT-seq and FLAMES to characterize full-length isoforms in single cells of human and mouse, identifying thousands of unannotated isoforms and linking them to functional modules and drug resistance mutations.