Sequence assembly demystified

N Nagarajan, M Pop - Nature Reviews Genetics, 2013 - nature.com
Advances in sequencing technologies and increased access to sequencing services have
led to renewed interest in sequence and genome assembly. Concurrently, new applications …

Next-generation sequence assembly: four stages of data processing and computational challenges

S El-Metwally, T Hamza, M Zakaria… - PLoS computational …, 2013 - journals.plos.org
Decoding DNA symbols using next-generation sequencers was a major breakthrough in
genomic research. Despite the many advantages of next-generation sequencers, eg, the …

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative map** approach

C Hahn, L Bachmann, B Chevreux - Nucleic acids research, 2013 - academic.oup.com
We present an in silico approach for the reconstruction of complete mitochondrial genomes
of non-model organisms directly from next-generation sequencing (NGS) data …

ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

SC Clark, R Egan, PI Frazier, Z Wang - Bioinformatics, 2013 - academic.oup.com
Motivation: Researchers need general purpose methods for objectively evaluating the
accuracy of single and metagenome assemblies and for automatically detecting any errors …

Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data

A Desai, VS Marwah, A Yadav, V Jha, K Dhaygude… - PloS one, 2013 - journals.plos.org
Next Generation Sequencing (NGS) is a disruptive technology that has found widespread
acceptance in the life sciences research community. The high throughput and low cost of …

A comprehensive study of de novo genome assemblers: current challenges and future prospective

AR Khan, MT Pervez, ME Babar… - Evolutionary …, 2018 - journals.sagepub.com
Background: Current advancements in next-generation sequencing technology have made
possible to sequence whole genome but assembling a large number of short sequence …

Perfluorobutane sulfonate exposure disrupted human placental cytotrophoblast cell proliferation and invasion involving in dysregulating preeclampsia related genes

WP Marinello, ZS Mohseni, SJ Cunningham… - The FASEB …, 2020 - Wiley Online Library
We reported that maternal PFBS, an emerging pollutant, exposure is positively associated
with preeclampsia which can result from aberrant trophoblasts invasion and subsequent …

Host subtraction, filtering and assembly validations for novel viral discovery using next generation sequencing data

GM Daly, RM Leggett, W Rowe, S Stubbs, M Wilkinson… - PloS one, 2015 - journals.plos.org
The use of next generation sequencing (NGS) to identify novel viral sequences from
eukaryotic tissue samples is challenging. Issues can include the low proportion and copy …

Archaeal communities: the microbial phylogenomic frontier

NO Medina-Chávez, M Travisano - Frontiers in Genetics, 2022 - frontiersin.org
Archaea are a unique system for investigating the diversity of life. There are the most diverse
group of organisms with the longest evolutionary history of life on Earth. Phylogenomic …

In Silico Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

X Zhou, D Peris, J Kominek… - G3: Genes …, 2016 - academic.oup.com
The availability of genomes across the tree of life is highly biased toward vertebrates,
pathogens, human disease models, and organisms with relatively small and simple …