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Microbial Genome Sequencing and Assembly Using Nanopore Sequencers
2023Microbial genomes are typically several million base pairs in length and are relatively easy to sequence and assemble into a single chromosome, given the advances in long-read sequencing platforms such as that of Oxford Nanopore Technologies. This chapter describes the experimental as well as computational steps in the sequencing and assembly of ...
Makoto, Taniguchi, Kazuma, Uesaka
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The Theory and Practice of Genome Sequence Assembly
Annual Review of Genomics and Human Genetics, 2015The current genomic revolution was made possible by joint advances in genome sequencing technologies and computational approaches for analyzing sequence data. The close interaction between biologists and computational scientists is perhaps most apparent in the development of approaches for sequencing entire genomes, a feat that would not be possible ...
Jared T, Simpson, Mihai, Pop
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Assembling Genomic DNA Sequences with PHRAP
Current Protocols in Bioinformatics, 2007AbstractThe PHRAP assembly program provides rapid comparison, alignment, and assembly of large sets of DNA sequences. PHRAP compares sequences by searching for pairs of perfectly matching “words” or sequence regions that meet certain criteria. If a match is found, PHRAP then tries to extend the alignment into overlapping sections called contigs.
Melissa, de la Bastide +1 more
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Genome sequence assembly: algorithms and issues
Computer, 2002Ultimately, genome sequencing seeks to provide an organism's complete DNA sequence. Automation of DNA sequencing allowed scientists to decode entire genomes and gave birth to genomics, the analytic and comparative study of genomes. Although genomes can include billions of nucleotides, the chemical reactions researchers use to decode the DNA are ...
Mihai Pop +2 more
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How to Sequence and Assemble Plant Genomes
2023Although nanopore sequencer is a great tool, many plant scientists have suffered from bad sequencing results, even though they have exactly followed the official protocol in preparing a library. This is because the protocol is not optimized for plant genomic DNA.
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Genome Assembler for Repetitive Sequences
2012The article presents a new algorithm for random DNA fragment assembly. The algorithm uses an extended de Bruijn graph that stores information of reads coverage. It is able to reconstruct consecutive repetitive sequences longer than reads and to process large amount of data provided by new generation sequencers.
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Crayfish genome sequencing and assembly
2023Identification of putative allergens in P ...
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Fusarium Genome Sequencing and Assembly
Fusarium is a genus of significant concern and interest. With the development of omics technologies, sequencing and assembling fungal genomes became widely available. To date, numerous Fusarium genomes were deposited in genomic databases. This chapter highlights the importance of studying Fusarium species and discusses the structure and peculiarities ...Ekaterina M, Dvorianinova +2 more
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From Sequence Mapping to Genome Assemblies
2014The development of "next-generation" high-throughput sequencing technologies has made it possible for many labs to undertake sequencing-based research projects that were unthinkable just a few years ago. Although the scientific applications are diverse, e.g., new genome projects, gene expression analysis, genome-wide functional screens, or epigenetics ...
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Sequencing and Assembly of the Pineapple Genome
2018Pineapple (Ananas comosus L.) is an important tropical fruit crop, not only because of its economic value but also due to its CAM photosynthesis that exhibits the highest water-use efficiency comparing to plants with C3 and C4 photosynthesis. The genome of pineapple variety F153 was sequenced using a combination of DNA sequencing technologies ...
Jishan Lin, Ray Ming
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