ArticleBMC genomics2018
Towards pan-genome read alignment to improve variation calling.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed.
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- Panaln: indexing pangenome for read alignment.Bioinformatics (Oxford, England) · 2025Article
- A gentle introduction to pangenomics.Briefings in bioinformatics · 2024Review
- Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests.LIPIcs : Leibniz international proceedings in informatics · 2024Article
- Measuring, visualizing, and diagnosing reference bias with biastools.Genome biology · 2024Article
- Suffix sorting via matching statistics.Algorithms for molecular biology : AMB · 2024Article
- Measuring, visualizing and diagnosing reference bias with biastools.bioRxiv : the preprint server for biology · 2024Article
- Chaining for accurate alignment of erroneous long reads to acyclic variation graphs.Bioinformatics (Oxford, England) · 2023Article
- Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses.Genome research · 2022Article
- MONI: A Pangenomic Index for Finding Maximal Exact Matches.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Gramtools enables multiscale variation analysis with genome graphs.Genome biology · 2021Article
- Building a Chinese pan-genome of 486 individuals.Communications biology · 2021Article
- Methods and Developments in Graphical Pangenomics.Journal of the Indian Institute of Science · 2021Review
- One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.PLoS computational biology · 2021Article
- Pangenome Graphs.Annual review of genomics and human genetics · 2020Review
- Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods.BMC genomics · 2020Article
- Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.PLoS computational biology · 2019Article
- Is it time to change the reference genome?Genome biology · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTypical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation.
resultsWe propose a new unified framework for variant calling with short-read data utilizing a representation of human genetic variation - a pan-genomic reference. We provide a modular pipeline that can be seamlessly incorporated into existing sequencing data analysis workflows. Our tool is open source and available online: https://gitlab.com/dvalenzu/PanVC .
conclusionsOur experiments show that by replacing a standard human reference with a pan-genomic one we achieve an improvement in single-nucleotide variant calling accuracy and in short indel calling accuracy over the widely adopted Genome Analysis Toolkit (GATK) in difficult genomic regions.
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