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

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Plant Comparative Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2512))

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Abstract

Hypothesized evolutionary insertions and deletions in nucleic acid sequences (indels) contain significant phylogenetic information and can be integrated in phylogenomic analyses. However, assemblies of short reads obtained from next-generation sequencing (NGS) technologies can contain errors that result in falsely inferred indels that need to be detected and omitted to avoid inclusion in phylogenetic analysis. Here, we detail the commands that comprise a new version of the NGS-Indel Coder pipeline, which was developed to validate indels using assembly read depth.

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Acknowledgments

This work was supported by NSF DEB awards 1457510/1457473 to MF and SCKS.

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Boutte, J., Fishbein, M., Straub, S.C.K. (2022). NGS-Indel Coder v2.0: A Streamlined Pipeline to Code Indel Characters in Phylogenomic Data. In: Pereira-Santana, A., Gamboa-Tuz, S.D., Rodríguez-Zapata, L.C. (eds) Plant Comparative Genomics. Methods in Molecular Biology, vol 2512. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2429-6_4

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  • DOI: https://doi.org/10.1007/978-1-0716-2429-6_4

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2428-9

  • Online ISBN: 978-1-0716-2429-6

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