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Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes
Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how va...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer US
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10276077/ https://www.ncbi.nlm.nih.gov/pubmed/36651964 http://dx.doi.org/10.1007/s00239-022-10083-z |
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author | Johnson, Milo S. Venkataram, Sandeep Kryazhimskiy, Sergey |
author_facet | Johnson, Milo S. Venkataram, Sandeep Kryazhimskiy, Sergey |
author_sort | Johnson, Milo S. |
collection | PubMed |
description | Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00239-022-10083-z. |
format | Online Article Text |
id | pubmed-10276077 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Springer US |
record_format | MEDLINE/PubMed |
spelling | pubmed-102760772023-06-18 Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes Johnson, Milo S. Venkataram, Sandeep Kryazhimskiy, Sergey J Mol Evol Review Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00239-022-10083-z. Springer US 2023-01-18 2023 /pmc/articles/PMC10276077/ /pubmed/36651964 http://dx.doi.org/10.1007/s00239-022-10083-z Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/ Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Review Johnson, Milo S. Venkataram, Sandeep Kryazhimskiy, Sergey Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes |
title | Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes |
title_full | Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes |
title_fullStr | Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes |
title_full_unstemmed | Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes |
title_short | Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes |
title_sort | best practices in designing, sequencing, and identifying random dna barcodes |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10276077/ https://www.ncbi.nlm.nih.gov/pubmed/36651964 http://dx.doi.org/10.1007/s00239-022-10083-z |
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