SHIMS 3.0: Highly efficient single-haplotype iterative mapping and sequencing using ultra-long nanopore reads
Name
journal.pone.0269692.pdf
Description
Published version
Size
1.94 MB
Format
Adobe PDF
Checksum (MD5)
bc33ee9e94888540880010ee7567f41c
Author(s)
Bellott, Daniel W
Cho, Ting-Jan
Jackson, Emily K
Skaletsky, Helen
Hughes, Jennifer F
Page, David C
Date Issued
2022
Journal
PLoS ONE
Publisher
Public Library of Science (PLoS)
Citation
Bellott, Daniel W, Cho, Ting-Jan, Jackson, Emily K, Skaletsky, Helen, Hughes, Jennifer F et al. 2022. "SHIMS 3.0: Highly efficient single-haplotype iterative mapping and sequencing using ultra-long nanopore reads." PLoS ONE, 17 (6).
Version
Final published version
Abstract
The reference sequence of structurally complex regions can only be obtained through a highly accurate clone-based approach that we call Single-Haplotype Iterative Mapping and Sequencing (SHIMS). In recent years, improvements to SHIMS have reduced the cost and time required by two orders of magnitude, but internally repetitive clones still require extensive manual effort to transform draft assemblies into reference-quality finished sequences. Here we describe SHIMS 3.0, using ultra-long nanopore reads to augment the Illumina data from SHIMS 2.0 assemblies and resolve internally repetitive structures. This greatly minimizes the need for manual finishing of Illumina-based draft assemblies, allowing a small team with no prior finishing experience to sequence challenging targets with high accuracy. This protocol proceeds from clone-picking to finished assemblies in 2 weeks for about $80 (USD) per clone. We recently used this protocol to produce reference sequence of structurally complex palindromes on chimpanzee and rhesus macaque X chromosomes. Our protocol provides access to structurally complex regions that would otherwise be inaccessible from whole-genome shotgun data or require an impractical amount of manual effort to generate an accurate assembly.
MIT Department
Massachusetts Institute of Technology. Department of Biology
Terms of Use
Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.1371/JOURNAL.PONE.0269692
