ArticleBMC bioinformatics2022
gcaPDA: a haplotype-resolved diploid assembler.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly.Nature methods · 2024Article
- From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).Briefings in bioinformatics · 2023Article
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Authors and funding
12 authors.
Funding
Abstract
backgroundGenerating chromosome-scale haplotype resolved assembly is important for functional studies. However, current de novo assemblers are either haploid assemblers that discard allelic information, or diploid assemblers that can only tackle genomes of low complexity.
resultsHere, Using robust programs, we build a diploid genome assembly pipeline called gcaPDA (gamete cells assisted Phased Diploid Assembler), which exploits haploid gamete cells to assist in resolving haplotypes. We demonstrate the effectiveness of gcaPDA based on simulated HiFi reads of maize genome which is highly heterozygous and repetitive, and real data from rice.
conclusionsWith applicability of coping with complex genomes and fewer restrictions on application than most of diploid assemblers, gcaPDA is likely to find broad applications in studies of eukaryotic genomes.
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Registered trials
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