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      Genome sequencing guide: An introductory toolbox to whole‐genome analysis methods

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          Abstract

          To fully appreciate genetics, one must understand the link between genotype (DNA sequence) and phenotype (observable characteristics). Advances in high‐throughput genomic sequencing technologies and applications, so‐called “‐omics,” have made genetic sequencing readily available across fields in biology from applications in non‐traditional study organisms to precision medicine. Thus, understanding these tools is critical for any biologist, especially those early in their career. This comprehensive review discusses the chronological development of different sequencing methods, the bioinformatics steps to analyzing this data, and social and ethical issues raised by these techniques that must be discussed and evaluated, including anticipatory guides and discussion questions for active engagement in the classroom. Additionally, the Supporting Information includes a case study to apply technical and ethical concepts from the text.

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          Most cited references54

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          Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference

          We introduce Salmon, a method for quantifying transcript abundance from RNA-seq reads that is accurate and fast. Salmon is the first transcriptome-wide quantifier to correct for fragment GC content bias, which we demonstrate substantially improves the accuracy of abundance estimates and the reliability of subsequent differential expression analysis. Salmon combines a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure.
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            Near-optimal probabilistic RNA-seq quantification.

            We present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases. We use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in <10 min on a standard laptop computer. This removes a major computational bottleneck in RNA-seq analysis.
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              Initial sequencing and analysis of the human genome.

              The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
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                Author and article information

                Contributors
                dethurtleschmidt@davidson.edu
                Journal
                Biochem Mol Biol Educ
                Biochem Mol Biol Educ
                10.1002/(ISSN)1539-3429
                BMB
                Biochemistry and Molecular Biology Education
                John Wiley & Sons, Inc. (Hoboken, USA )
                1470-8175
                1539-3429
                11 August 2021
                Sep-Oct 2021
                : 49
                : 5 ( doiID: 10.1002/bmb.v49.5 )
                : 815-825
                Affiliations
                [ 1 ] Department of Biology Ithaca College Ithaca New York USA
                [ 2 ] Department of Biology Davidson College Davidson North Carolina USA
                Author notes
                [*] [* ] Correspondence

                Deborah M. Thurtle‐Schmidt, Department of Biology, Box 7118, Davidson College, Davidson, NC 28035, USA.

                Email: dethurtleschmidt@ 123456davidson.edu

                Author information
                https://orcid.org/0000-0002-1231-5531
                https://orcid.org/0000-0002-9747-9585
                Article
                BMB21561
                10.1002/bmb.21561
                9291972
                34378845
                1d0cd46e-b8ee-4b45-9de1-e8b626946623
                © 2021 The Authors. Biochemistry and Molecular Biology Education published by Wiley Periodicals LLC on behalf of International Union of Biochemistry and Molecular Biology

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 17 June 2021
                : 18 December 2020
                : 09 July 2021
                Page count
                Figures: 5, Tables: 0, Pages: 11, Words: 6734
                Funding
                Funded by: Davidson College
                Categories
                Topical Review
                Topical Review
                Custom metadata
                2.0
                September/October 2021
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.7 mode:remove_FC converted:18.07.2022

                Education
                bioinformatics,ethics,genomics,sequencing
                Education
                bioinformatics, ethics, genomics, sequencing

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