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ReMILO: reference assisted misassembly detection algorithm using short and long reads.

Ergude Bao1,2, Changjin Song1, Lingxiao Lan1

  • 1Software Engineering Research Center, School of Software Engineering, Beijing Jiaotong University, Beijing 100044, China.

Bioinformatics (Oxford, England)
|September 30, 2017
PubMed
Summary
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ReMILO, a novel algorithm, accurately detects genome assembly misassemblies using short and long sequencing reads. This tool improves genomic data reliability by identifying both extensive and local errors in assemblies.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome assembly from short reads can introduce misassemblies, compromising downstream analyses.
  • Reference genomes and long reads offer potential for detecting these assembly errors.

Purpose of the Study:

  • To introduce ReMILO, a reference-assisted algorithm for detecting misassemblies in genome assemblies.
  • To leverage both short and long sequencing reads for enhanced misassembly detection.

Main Methods:

  • ReMILO aligns short reads to contigs and a reference genome.
  • It utilizes a red-black multipositional de Bruijn graph to identify misassemblies.
  • Contigs are also aligned to long reads to detect discrepancies.

Main Results:

Related Experiment Videos

  • ReMILO detected 41.8-77.9% of extensive and 33.6-54.5% of local misassemblies in human chromosome 14 short-read assemblies.
  • For hybrid assemblies of S. pastorianus, ReMILO identified 60.6-70.9% of extensive and 28.6-54.0% of local misassemblies.

Conclusions:

  • ReMILO effectively detects misassemblies in genome assemblies using combined short and long read data.
  • The algorithm enhances the accuracy and reliability of genomic data analysis.