Improving ancient DNA genome assembly [PDF]
PeerJ, 2017 Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used.
Alexander Seitz, Kay Nieselt
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ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
BMC Bioinformatics, 2021 Background Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in
Zachary Deng, Eric Delwart
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Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. [PDF]
PLoS ONE, 2016 Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies.
Loren A Honaas +9 more
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Exploiting sparseness in de novo genome assembly [PDF]
BMC Bioinformatics, 2012 The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k- mers as nodes and the links between these nodes allows the de novo ...
Chengxi Ye +4 more
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Accurate long-read de novo assembly evaluation with Inspector
Genome Biology, 2021 Long-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors.
Yu Chen +4 more
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Comparative analysis of de novo transcriptome assembly [PDF]
Science China Life Sciences, 2013 The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis. A fast algorithm, de Bruijn graph has been successfully used for genome DNA de novo assembly; nevertheless, its performance for transcriptome assembly is unclear. In this study, we used both simulated and real RNA-Seq
Clarke, Kaitlin +4 more
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Challenges and advances for transcriptome assembly in non-model species. [PDF]
PLoS ONE, 2017 Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly.
Arnaud Ungaro +6 more
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De novo assembly of short sequence reads [PDF]
Briefings in Bioinformatics, 2010 A new generation of sequencing technologies is revolutionizing molecular biology. Illumina's Solexa and Applied Biosystems' SOLiD generate gigabases of nucleotide sequence per week. However, a perceived limitation of these ultra-high-throughput technologies is their short read-lengths.
Konrad H. Paszkiewicz +1 more
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Reference-guided de novo assembly approach improves genome reconstruction for related species
BMC Bioinformatics, 2017 Background The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions ...
Heidi E. L. Lischer, Kentaro K. Shimizu
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Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance [PDF]
, 2011 Background: Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms.
Wheat, Christopher W. +10 more
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