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lsvtool source code

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posted on 2023-10-03, 09:06 authored by Pontus HöjerPontus Höjer, Afshin Ahmadian, Parham Pourbozorgi, Tobias Frick, Hooman Aghelpasand, Humam Siga, Marcel Martin

Archive of lsvtool for submission of manuscript: "BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies".


Abstract

Linked-read sequencing promises a one-method approach for genome-wide insights including single nucleotide variants (SNVs), structural variants, and haplotyping. Here we present Barcode Linked Reads (BLR), an open-source haplotyping pipeline capable of handling millions of barcodes and data from multiple linked-read technologies including DBS, 10x Genomics, TELL-seq and stLFR. We used BLR to explore the impact of using single versus multiple genomic DNA molecules per droplet in the DBS technology. While both approaches, in spite of short molecule lengths, yielded megabase-scale phase blocks with low switch-error rates, single-molecule resolution improved phasing contiguity. In a high-coverage data, combining the two DBS datasets, large structural variants showed concordance with 10x Genomics and PacBio. In addition, the phasing of protein-coding genes showed that most (93.8%) matched phasing from a GIAB benchmark set. Comparing Long Ranger to BLR on 10x Genomics data showed a four-time increase in phase block N50 for BLR while maintaining low switch-error rates. For TELL-Seq and stLFR linked reads, BLR generated longer or similar phase block lengths and low switch error rates compared to results presented in the original publications for the respective technologies. In conclusion, BLR presents a flexible workflow for comprehensive haplotype analysis of linked reads from multiple platforms.

Funding

Erling Persson Family Foundation

Olle Engkvist Foundation (191-0475 and 193-0605)

Swedish Research Council (VR) (2018-06228)

Stockholm County Council (20190989)

KTH-SFO SciLifeLab Funding (SciLifeLab Postdoc Program and SciLifeLab RED project)

Knut and Alice Wallenberg Foundation

History

Publisher

KTH Royal Institute of Technology

Contact email

phojer@kth.se

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