Alpseq: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing

Zeglinski, K; Schuster, J; Sa, JD; Adair, A; Deng, J; Pymm, P; Ritchie, ME; Bowden, R; Tham, WH; Gouil, Q

Author(s): Zeglinski, K; Schuster, J; Sa, JD; Adair, A; Deng, J; Pymm, P; Ritchie, ME; Bowden, R; Tham, WH; Gouil, Q;
Details: Publication Year 2026-12-31,Volume 18,Issue #1,Page 2623326
Journal Title: mAbs
Abstract: Nanobodies have emerged as promising tools for many biotechnological applications due to their small size, high stability and remarkable binding specificity. Next-Generation Sequencing (NGS) enables deep profiling of large nanobody libraries and panning campaigns; however, the scale and diversity of nanobody NGS datasets presents a significant bioinformatic challenge. To this end, we have developed alpseq, an optimized, open-source software pipeline designed specifically for the efficient and accurate processing of NGS data from nanobody libraries and panning campaigns. alpseq is also paired with a PCR-free sequencing library preparation protocol to allow researchers to easily generate their own data while avoiding biases. The alpseq software pipeline is composed of two parts: a pre-processing module written in Nextflow efficiently handles raw nanobody reads in a single line of code. These results are then fed into the analysis module, which contains a comprehensive suite of functions for quality control, diversity analysis, identification of enriched sequences and clustering. alpseq also creates a user-friendly interactive report which empowers scientists to explore their data without the need for extensive bioinformatic experience. Sophisticated panning campaign designs are supported, such as replicates and comparisons between different pans to find cross-binding leads. alpseq thus generates insights into the nanobody selection process and delivers a list of lead candidates for further experimental validation and downstream applications. alspeq is available at https://github.com/kzeglinski/alpseq.
Publisher: Taylor & Francis
Keywords: *Single-Domain Antibodies/genetics/immunology; *High-Throughput Nucleotide Sequencing/methods; *Software; Humans; Workflow; *Computational Biology/methods; Bioinformatics; Illumina; Nextflow; biologics; biopanning; display technologies; nanobodies; next-generation sequencing
Research Division(s): Genetics and Gene Regulation; Infection and Global Health; New Medicines and Diagnostics
PubMed ID: 41631412
Publisher's Version: https://doi.org/10.1080/19420862.2026.2623326
Open Access at Publisher's Site: https://doi.org/10.1080/19420862.2026.2623326
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2026-02-09 09:18:24

Last Modified: 2026-02-09 09:23:24