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The untapped potential of short-read sequencing in biodiversity research
Trends in GeneticsThe power of short-read DNA sequencing in biodiversity research and evolutionary genomics is rapidly growing due to advances in technology and bioinformatics. Short-read sequencing offers powerful solutions for taxonomic identification, biomass estimation, and phylogenetic reconstruction.
Christoph Bleidorn +2 more
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Short Read Mapping for Exome Sequencing
2013Mapping short reads to the reference genome is very often the prerequisite for applications utilizing the next-generation sequencing technologies. A dozen of software tools developed for this purpose have been widely used. But many practical issues remained when utilizing them to build a computational pipeline for downstream analyses.
Zhang, X +4 more
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Mapping short reads to a genomic sequence with circular structure
Proceedings of the 10th IEEE International Conference on Information Technology and Applications in Biomedicine, 2010Constant advances in DNA sequencing technologies are turning whole-genome sequencing into a routine procedure, resulting in massive amounts of data that need to be processed. Tens of gigabytes of data, in the form of short sequences (reads), need to be mapped back onto reference sequences, a few gigabases long.
Flouri, Tomas +3 more
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Short read sequencing in studies of natural variation and adaptation
Current Opinion in Plant Biology, 2013Today's high throughput sequencing approaches, coupled with equally revolutionary advances in bioinformatics, allow us to describe and analyze genomes in unprecedented detail. Short Read Sequencing (SRS) approaches have been especially instrumental in bringing genomic analysis to a wide range of questions and species in plant biology.
Ben, Hunter +2 more
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Probability Model for Boundaries of Short-Read Sequencing
2012 International Conference on Advances in Computing and Communications, 2012The need for sequencing DNA has been growing tremendously over the past few years. Current next-generation sequencing techniques produce huge amounts of data but time and money remain limiting factors for researchers. Given a DNA sample, it is essential to produce a sufficient number of reads to create or recreate a digital representation of the DNA ...
Florian Schatz +2 more
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Analysis of Short-read Aligners using Genome Sequence Complexity
2020 12th International Conference on Knowledge and Systems Engineering (KSE), 2020Next generation sequencing technologies have the capability to provide large numbers of short reads inexpensively and accurately. Researchers have proposed many different methods to align short reads to reference genomes. Nevertheless, long repeats, which are known to be abundant in eukaiyotic genomes, have caused considerable difficulty for genome ...
Quang Tran 0002 +4 more
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RNA Sequencing Protocols for Short-Read Sequencing
RNA sequencing (RNA-seq) methodologies allow the discovery of novel variants and transcripts. These comprise three general steps: (1) capture of RNA species of interest, (2) conversion of RNA to complementary DNA (cDNA), and (3) modification of cDNA to fit the sequencing platform.Laura, Vasquez-Velez +2 more
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Efficient short-read sequencing on long-read sequencers
2020We present SMURF-seq, a protocol to efficiently sequence short DNA molecules on a long-read sequencer by randomly ligating them to form long molecules. Applying SMURF-seq using the highly portable and inexpensive Oxford Nanopore MinION yields up to 30 fragments per read, providing an average of 6.2 and up to 7.5 million mappable fragments per run ...
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Detecting Signatures of TE Polymorphisms in Short-Read Sequencing Data
2021Transposable elements (TEs) are an important cause of evolutionary change and functional diversity, yet they are routinely discarded in the first steps of many analyses. In this chapter we show how, given a reference genome, TEs can be incorporated fairly easily into functional and evolutionary studies.
Stritt, Christoph, Roulin, Anne C
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An algorithm for mapping short reads to a dynamically changing genomic sequence
2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2010The constant advances in sequencing technology have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads), during a single experiment, and with a much lower cost than previously possible.
Tomás Flouri +3 more
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