Linked-read analysis identifies mutations in single-cell DNA-sequencing data.
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ABSTRACT:
SUBMITTER: Bohrson CL
PROVIDER: S-EPMC6900933 | biostudies-literature | 2019 Apr
REPOSITORIES: biostudies-literature
Publications
Linked-read analysis identifies mutations in single-cell DNA-sequencing data.
Bohrson Craig L CL Barton Alison R AR Lodato Michael A MA Rodin Rachel E RE Luquette Lovelace J LJ Viswanadham Vinay V VV Gulhan Doga C DC Cortés-Ciriano Isidro I Sherman Maxwell A MA Kwon Minseok M Coulter Michael E ME Galor Alon A Walsh Christopher A CA Park Peter J PJ
Nature genetics 20190318 4
Whole-genome sequencing of DNA from single cells has the potential to reshape our understanding of mutational heterogeneity in normal and diseased tissues. However, a major difficulty is distinguishing amplification artifacts from biologically derived somatic mutations. Here, we describe linked-read analysis (LiRA), a method that accurately identifies somatic single-nucleotide variants (sSNVs) by using read-level phasing with nearby germline heterozygous polymorphisms, thereby enabling the chara ...[more]
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Project description:SummaryLinked-read sequencing generates synthetic long reads which are useful for the detection and analysis of structural variants (SVs). The software associated with 10× Genomics linked-read sequencing, Long Ranger, generates the essential output files (BAM, VCF, SV BEDPE) necessary for downstream analyses. However, to perform downstream analyses requires the user to customize their own tools to handle the unique features of linked-read sequencing data. Here, we describe gemtools, a collection of tools for the downstream and in-depth analysis of SVs from linked-read data. Gemtools uses the barcoded aligned reads and the Megabase-scale phase blocks to determine haplotypes of SV breakpoints and delineate complex breakpoint configurations at the resolution of single DNA molecules. The gemtools package is a suite of tools that provides the user with the flexibility to perform basic functions on their linked-read sequencing output in order to address even more questions.Availability and implementationThe gemtools package is freely available for download at: https://github.com/sgreer77/gemtools.Supplementary informationSupplementary data are available at Bioinformatics online.
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