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Associated Chromosome Trap for Identifying Long-range DNA Interactions
Published on: April 23, 2011
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Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.
Nicholas H Putnam1, Brendan L O'Connell2, Jonathan C Stites1
1Dovetail Genomics LLC, Santa Cruz, California 95060, USA;
Genome Research
|February 6, 2016
Summary
We present a simpler Chicago (proximity ligation) method for highly accurate de novo genome assembly using reconstituted chromatin. This approach significantly improves genome scaffolding contiguity for both human and alligator genomes.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- De novo genome assembly from short-read data faces challenges in achieving long-range accuracy and contiguity.
- Proximity ligation of DNA in living tissue has shown promise in improving genome assembly scaffolding.
Purpose of the Study:
- To introduce a simpler and effective method for long-range, accurate de novo genome assembly.
- To develop a robust software pipeline for analyzing proximity ligation data and improving genome scaffolds.
Main Methods:
- Developed the Chicago method using in vitro reconstituted chromatin for proximity ligation.
- Generated Chicago data sets from human DNA.
- Created the HiRise software pipeline for data analysis, quality control, and scaffold generation.
Main Results:
- Achieved a highly accurate de novo assembly and scaffolding of a human genome with a scaffold N50 of 20 Mbp.
- Significantly improved the American alligator genome assembly, increasing scaffold N50 from 508 kbp to 10 Mbp using a single Chicago library and sequencing lane.
Conclusions:
- The Chicago method offers a simpler, effective approach to generating long-range, accurate genome scaffolds.
- This technique substantially enhances genome assembly contiguity and accuracy, applicable to both novel assemblies and improving existing ones.
