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Method Article
Ou Wang
BGI-Shenzhen
Corresponding Author
Brock Peters
Advanced Genomics Technology Lab, Complete Genomics Inc.
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Advances in genome sequencing continue to decrease cost and improve quality. However, the diploid information found in most genomes is still lost by the most common sequencing methods. There are several methods currently available for obtaining this haplotype information. However, most of these methods are either time consuming, require expensive equipment and reagents, or both. Here we describe single tube long fragment read (stLFR), a simple barcoded bead-based process capable of near perfect whole genome variant calling and haplotyping. Our method uses equipment available in nearly all molecular biology laboratories and costs approximately 30 dollars a sample. In addition, the data generated from this process is capable of detecting and phasing structural variations and scaffolding contigs. We expect in the future that this process will enable affordable diploid de novo assembly.
Keywords
stLFR, co-barcoded reads, de novo assembly, haplotyping, NGS
Figure 1
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Figure 4
Employees of BGI and Complete Genomics have stock holdings in BGI.
This is a list of supplementary files associated with this preprint. Click to download.
- supplement0.pdf
Supplementary Figure 1 Barcode sequence assembly Three ligations are necessary to generate ~3.6 billion different barcodes. The expected sequence at each step of the barcode assembly is displayed.
- supplement0.xlsx
Supplementary Materials Supplementary Materials
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An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Ou Wang
BGI-Shenzhen
Corresponding Author
Brock Peters
Advanced Genomics Technology Lab, Complete Genomics Inc.
Corresponding Author
Version History
CURRENT STATUS: Posted
Version 1
Posted 11 Oct, 2018
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Advances in genome sequencing continue to decrease cost and improve quality. However, the diploid information found in most genomes is still lost by the most common sequencing methods. There are several methods currently available for obtaining this haplotype information. However, most of these methods are either time consuming, require expensive equipment and reagents, or both. Here we describe single tube long fragment read (stLFR), a simple barcoded bead-based process capable of near perfect whole genome variant calling and haplotyping. Our method uses equipment available in nearly all molecular biology laboratories and costs approximately 30 dollars a sample. In addition, the data generated from this process is capable of detecting and phasing structural variations and scaffolding contigs. We expect in the future that this process will enable affordable diploid de novo assembly.
Figure 1
Figure 2
Figure 3
Figure 4
Employees of BGI and Complete Genomics have stock holdings in BGI.
This is a list of supplementary files associated with this preprint. Click to download.
- supplement0.pdf
Supplementary Figure 1 Barcode sequence assembly Three ligations are necessary to generate ~3.6 billion different barcodes. The expected sequence at each step of the barcode assembly is displayed.
- supplement0.xlsx
Supplementary Materials Supplementary Materials
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