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De Novo Transcriptome Assembly in Polyploid Species
2017In the absence of a reference genome, the ultimate goal of a de novo transcriptome assembly is to accurately and comprehensively reconstruct the set of messenger RNA transcripts represented in the sample. Non-reference assembly of the transcriptome of polyploid species poses a particular challenge because of the presence of homeologs that are difficult
Juan J, Gutierrez-Gonzalez +1 more
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Evaluation of nine popular de novo assemblers in microbial genome assembly
Journal of Microbiological Methods, 2017Next generation sequencing (NGS) technologies are revolutionizing biology, with Illumina being the most popular NGS platform. Short read assembly is a critical part of most genome studies using NGS. Hence, in this study, the performance of nine well-known assemblers was evaluated in the assembly of seven different microbial genomes. Effect of different
Esmaeil, Forouzan +3 more
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2011
An imperative first step in the characterization of a species or individual is the sequencing and subsequent assembly and analysis of its genome. High-throughput sequencing technology has ushered in a new way of thinking about this fundamental undertaking. Next-generation sequencing machines produce reads through highly parallel operation and produce a
Douglas W. Bryant, Todd C. Mockler
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An imperative first step in the characterization of a species or individual is the sequencing and subsequent assembly and analysis of its genome. High-throughput sequencing technology has ushered in a new way of thinking about this fundamental undertaking. Next-generation sequencing machines produce reads through highly parallel operation and produce a
Douglas W. Bryant, Todd C. Mockler
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Parallelization of the Trinity Pipeline for De Novo Transcriptome Assembly
2014 IEEE International Parallel & Distributed Processing Symposium Workshops, 2014This paper details a distributed-memory implementation of Chrysalis, part of the popular Trinity workflow used for de novo transcripto me assembly. We have implemented changes to Chrysalis, which was previously multi-threaded for shared-memory architectures, to change it to a hybrid implementation which uses both MPI and OpenMP.
Vipin Sachdeva +3 more
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Unraveling the mechanism of de novo nucleosome assembly
Science Bulletin, 2023Na, Yang, Zhenyu, Yu
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Towards accurate de novo assembly for genomes with repeats
2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2017De novo genome assemblers designed for short k-mer length or using short raw reads are unlikely to recover complex features of the underlying genome, such as repeats hundreds of bases long. We implement a stochastic machine-learning method which obtains accurate assemblies with repeats and self-validates assemblies via consensus.
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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Nature Methods, 2021Gregory Concepción +2 more
exaly
Algorithms for de novo assembly of large genomes
2019Tehnologije za sekvenciranje genoma nisu u mogućnosti interpretirati DNA molekule u cijelosti te je to dovelo do razvoja računalnih metoda koje spajaju kratke fragmente u procesu koji podsjeća na rješavanje slagalica. Alati namijenjeni za ovaj problem nazivaju se asembleri čiji je dizajn baziran na pretpostavci da slični fragmenti potječu iz iste ...
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TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
Molecular Ecology Resources, 2022Nicola Conci +2 more
exaly
Approaches to DNA de novo Assembly
2013DNA is the basic building block of all known life, accounting for all the diversities in nature. Determining the DNA of an individual organism is performed through a process called DNA sequencing. Although several different sequencing technologies do exist, they are limited and are able to acquire relatively short sequence reads.
Šikić, Mile +2 more
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