ArticleScientific reports2020
Improving read alignment through the generation of alternative reference via iterative strategy.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Integrative genomic analysis and gene expression patterns reveal a cardio-neuroendocrine signaling network for heat adaptation in geographically diverse chickens.Poultry science · 2026Article
- Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits.Nature communications · 2025Article
- Genomic Insights into the Origin, High Fecundity and Environmental Adaptation of Hu Sheep.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genome-wide analyses reveal intricate genetic mechanisms underlying egg production efficiency in chickens.Journal of animal science and biotechnology · 2025Article
- GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes.Genomics, proteomics & bioinformatics · 2025Article
- Genetic traceability, conservation effectiveness, and selection signatures analysis based on ancestral information: a case study of Beijing-You chicken.BMC genomics · 2025Article
- Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex.Horticulture research · 2024Article
- Characterization of complex structural variation in theFrontiers in pharmacology · 2023Article
- Whole-genome analysis reveals the hybrid formation of Chinese indigenous DHB pig following human migration.Evolutionary applications · 2022Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There is generally one standard reference sequence for each species. When extensive variations exist in other breeds of the species, it can lead to ambiguous alignment and inaccurate variant calling and, in turn, compromise the accuracy of downstream analysis. Here, with the help of the FPGA hardware platform, we present a method that generates an alternative reference via an iterative strategy to improve the read alignment for breeds that are genetically distant to the reference breed. Compared to the published reference genomes, by using the alternative reference sequences we built, the mapping rates of Chinese indigenous pigs and chickens were improved by 0.61-1.68% and 0.09-0.45%, respectively. These sequences also enable researchers to recover highly variable regions that could be missed using public reference sequences. We also determined that the optimal number of iterations needed to generate alternative reference sequences were seven and five for pigs and chickens, respectively. Our results show that, for genetically distant breeds, generating an alternative reference sequence can facilitate read alignment and variant calling and improve the accuracy of downstream analyses.
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