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- W4225426767 abstract "With the advancement of long-read sequencing technologies and associated bioinformatics tools, it has now become possible to de novo assemble complex plant genomes with unrivalled contiguity, completeness and correctness. As read lengths can surpass repeat lengths, the ability to assemble genomes de novo has dramatically improved, whereby complex plant genomes of widely variable sizes and repeat content have highly benefited. Despite these improvements, challenges remain in performing de novo assembly, namely in developing a reliable workflow and in tool choice. Here we present a protocol collection of bioinformatic workflows detailing plant genome assembly using Oxford Nanopore Technologies long-reads with a de novo assembler (Canu), syntenic or Hi-C scaffolding, and RNA and/or gene homology-based annotation. We have developed and tested these protocols on multiple plant genomes. Using these protocols with sufficient coverage of long-reads, a highly contiguous, complete, and correct plant genome can be assembled. These genomes can further genomic research into structural variation among groups, and SNP genotyping and association studies among populations." @default.
- W4225426767 created "2022-05-05" @default.
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- W4225426767 date "2022-03-21" @default.
- W4225426767 modified "2023-10-18" @default.
- W4225426767 title "Plant assemble - Plant de novo genome assembly: annotation v2" @default.
- W4225426767 doi "https://doi.org/10.17504/protocols.io.b6hfrb3n" @default.
- W4225426767 hasPublicationYear "2022" @default.
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