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lamassemble: Multiple Alignment and Consensus Sequence of Long Reads.

Martin C Frith1,2,3, Satomi Mitsuhashi4,5, Kazutaka Katoh6,7

  • 1Artificial Intelligence Research Center, AIST, Tokyo, Japan. mcfrith@edu.k.u-tokyo.ac.jp.

Methods in Molecular Biology (Clifton, N.J.)
|December 8, 2020
PubMed
Summary
This summary is machine-generated.

Long DNA and RNA sequencing reads contain errors. The lamassemble tool merges overlapping reads to create accurate consensus sequences, improving analysis of disease-related genetic regions.

Keywords:
DotplotGenomic variationsLASTMAFFTNanoporePacBioParalogyRepeat expansion diseaseStrand-asymmetric error patternlast-train

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Long-read sequencing technologies like nanopore and PacBio offer significant applications but produce raw reads with high error rates.
  • Accurate DNA and RNA sequences are crucial for various biological and medical research areas.

Purpose of the Study:

  • To introduce lamassemble, a novel tool for improving the accuracy of long DNA and RNA reads.
  • To enable more reliable analysis of specific genomic regions, including those associated with diseases.

Main Methods:

  • lamassemble aligns multiple overlapping long reads (up to ~1000) from nanopore or PacBio sequencing.
  • It generates a consensus sequence by integrating information from these aligned reads.

Main Results:

  • The consensus sequences produced by lamassemble are significantly more accurate than individual raw reads.
  • This method effectively reduces sequencing errors inherent in long-read technologies.

Conclusions:

  • lamassemble provides a valuable method for error correction in long DNA and RNA sequencing reads.
  • The tool enhances the utility of long-read sequencing for studying complex genomic regions and disease mutations.