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NGS-Indel Coder v2.0: A Streamlined Pipeline to Code Indel Characters in Phylogenomic Data.

Julien Boutte1, Mark Fishbein2, Shannon C K Straub3

  • 1Department of Biology, Hobart and William Smith Colleges, Geneva, NY, USA. boutte.julien@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|July 11, 2022
PubMed
Summary

This study introduces NGS-Indel Coder, a pipeline to validate evolutionary insertions and deletions (indels) in nucleic acid sequences. It uses read depth to filter out sequencing errors, improving phylogenetic analysis accuracy.

Keywords:
Character codingGapsIQ-TREEInsertion-deletionNGS read depthPhylogenySNP-detectionTarget capture sequencing

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Insertions and deletions (indels) in nucleic acid sequences provide crucial phylogenetic information.
  • Next-generation sequencing (NGS) assemblies can introduce errors, leading to false indel inferences.
  • Inaccurate indels can compromise the reliability of phylogenomic analyses.

Purpose of the Study:

  • To present an updated version of the NGS-Indel Coder pipeline.
  • To validate hypothesized evolutionary indels using assembly read depth.
  • To enhance the accuracy of phylogenomic analyses by filtering erroneous indels.

Main Methods:

  • Development and application of the NGS-Indel Coder pipeline.
  • Utilizing assembly read depth as a metric for indel validation.
  • Integration of the pipeline into phylogenomic workflows.

Main Results:

  • The NGS-Indel Coder pipeline effectively identifies and validates indels.
  • Read depth analysis successfully distinguishes true indels from sequencing errors.
  • The pipeline aids in the accurate curation of indel data for phylogenetics.

Conclusions:

  • The updated NGS-Indel Coder pipeline is a valuable tool for phylogenomic research.
  • Accurate indel validation is essential for robust evolutionary inference.
  • This method improves the reliability of phylogenetic reconstructions based on NGS data.