Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists

Recent advances in next-generation sequencing technologies have paved the path for a considerable amount of sequencing data at a relatively low cost. This has revolutionized the genomics and transcriptomics studies. However, different challenges are now created in handling such data with available b...

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Bibliographic Details
Published in:Scientific reports Vol. 10; no. 1; p. 18236
Main Authors: Naranpanawa, D. N. U., Chandrasekara, C. H. W. M. R. B., Bandaranayake, P. C. G., Bandaranayake, A. U.
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 26.10.2020
Nature Publishing Group
Subjects:
631/114/1314
631/114/2164
631/114/2184
631/114/2398
631/114/2400
631/114/2401
631/114/2785
631/114/794
Bioinformatics
Biologists
Computational Biology - methods
Computer programs
Databases, Genetic - statistics & numerical data
Gene expression
Genomics - methods
High-Throughput Nucleotide Sequencing - methods
Humanities and Social Sciences
Microsatellite Repeats
multidisciplinary
Next-generation sequencing
Santalum - genetics
Science
Science (multidisciplinary)
Sequence Analysis, DNA - methods
Simple sequence repeats
Software
Transcriptome
Workflow
ISSN:2045-2322, 2045-2322
Online Access:Get full text
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Summary:Recent advances in next-generation sequencing technologies have paved the path for a considerable amount of sequencing data at a relatively low cost. This has revolutionized the genomics and transcriptomics studies. However, different challenges are now created in handling such data with available bioinformatics platforms both in assembly and downstream analysis performed in order to infer correct biological meaning. Though there are a handful of commercial software and tools for some of the procedures, cost of such tools has made them prohibitive for most research laboratories. While individual open-source or free software tools are available for most of the bioinformatics applications, those components usually operate standalone and are not combined for a user-friendly workflow. Therefore, beginners in bioinformatics might find analysis procedures starting from raw sequence data too complicated and time-consuming with the associated learning-curve. Here, we outline a procedure for de novo transcriptome assembly and Simple Sequence Repeats (SSR) primer design solely based on tools that are available online for free use. For validation of the developed workflow, we used Illumina HiSeq reads of different tissue samples of Santalum album (sandalwood), generated from a previous transcriptomics project. A portion of the designed primers were tested in the lab with relevant samples and all of them successfully amplified the targeted regions. The presented bioinformatics workflow can accurately assemble quality transcriptomes and develop gene specific SSRs. Beginner biologists and researchers in bioinformatics can easily utilize this workflow for research purposes.
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ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-020-75270-8