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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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Orthopoxvirus Genome Sequencing, Assembly, and Analysis
Poxviruses have exceptionally large genomes compared to most other viruses, which represent unique challenges to sequencing and assembly due to complex features such as repeat elements and low complexity sequences. The 2022 global mpox outbreak led to an unprecedented level of poxvirus sequencing as public health and research institutions faced with ...Crystal M, Gigante +2 more
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Arthropod Genome Sequencing and Assembly Strategies
2018As in any endeavor, the strategy applied to a genome project can mean the difference between success and failure. This is especially important when limited funding often means only a single approach may be tried at a given time. Although the advance of all areas of genomics and transcriptomics in recent years has led to an embarrassment of riches ...
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Strategy for Genome Sequencing Analysis and Assembly for Comparative Genomics of Pseudomonas Genomes
2014Bacterial genome sequencing has developed rapidly in the last decade and has become a primary method for analyzing the genomic basis of differences in phenotype between strains as well as being a valuable tool for public health epidemiology. This chapter provides a comprehensive workflow for bacterial genome sequencing from experimental design to data ...
Jeukens, Julie +3 more
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Whole-Genome Sequencing for Comparative Genomics and De Novo Genome Assembly
2015Next-generation sequencing technologies for whole-genome sequencing of mycobacteria are rapidly becoming an attractive alternative to more traditional sequencing methods. In particular this technology is proving useful for genome-wide identification of mutations in mycobacteria (comparative genomics) as well as for de novo assembly of whole genomes ...
Benjak A, Sala C, Hartkoorn RC
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Anas Genome sequencing and assembly
2017Domestic ducks were tamed from mallard or the descendant of mallard and spot-billed duck. Here we presented the mallard and the spot-billed genomes, and performed whole-genome sequencing on eight domestic duck breeds and eight wild duck species. And with these data we unravel a distinct evolutionary pattern of ducks and two wild duck de novo genomes ...
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The landscape of genome sequencing and assembling in plants
Functional & Integrative Genomics, 2022Wanying, Liu, Baohong, Zhang
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GiSA: A Grid System for Genome Sequences Assembly
2004Sequencing genomes is a fundamental aspect of biological research. Shotgun sequencing, since introduced by Sanger et al [2], has remained the mainstay in the research field of genome sequence assembly. This method randomly obtains sequence reads (e.g.
Jun Tang +4 more
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