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HALC: High throughput algorithm for long read error correction.

Ergude Bao1,2, Lingxiao Lan3

  • 1School of Software Engineering, Beijing Jiaotong University, 3 Shangyuan Residence, Haidian District, Beijing, 100044, China. baoe@bjtu.edu.cn.

BMC Bioinformatics
|April 7, 2017
PubMed
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HALC is a new algorithm that corrects errors in PacBio SMRT long reads with high throughput. It improves genome assembly contig length and accuracy by reducing sequencing errors without discarding bases.

Area of Science:

  • Genomics
  • Bioinformatics
  • Sequencing Technology

Background:

  • Third-generation PacBio SMRT long reads offer improved read length but have ~15% error rate.
  • Existing error correction algorithms reduce errors to 1% but lower throughput by discarding uncorrected bases.
  • Loss of bases can limit downstream assembly completeness and analysis accuracy.

Purpose of the Study:

  • Introduce HALC, a high-throughput algorithm for long read error correction.
  • Improve genome assembly contig length and accuracy by minimizing data loss during error correction.

Main Methods:

  • HALC aligns long reads to short read contigs with low identity requirements.
  • It constructs a contig graph and uses long read support for validation and correction.
Keywords:
Error correctionPacBio long readsThroughput

Related Experiment Videos

  • Refines corrected regions using initial short reads to address uncorrected segments.

    • Main Results:

    • HALC achieved 6.7-41.1% higher throughput than existing algorithms on E. coli, A. thaliana, and M. zebra datasets.
    • Maintained comparable accuracy while significantly increasing throughput.
    • HALC-corrected long reads resulted in 11.4-60.7% longer assembled contigs.

    Conclusions:

    • HALC offers a high-throughput solution for long read error correction.
    • The software is freely available for download.
    • Enables more complete and accurate genome assemblies from long read sequencing data.