Opportunities and challenges in long-read sequencing data analysis

SL Amarasinghe, S Su, X Dong, L Zappia, ME Ritchie… - Genome biology, 2020 - Springer
Long-read technologies are overcoming early limitations in accuracy and throughput,
broadening their application domains in genomics. Dedicated analysis tools that take into …

Structural variation in the sequencing era

SS Ho, AE Urban, RE Mills - Nature Reviews Genetics, 2020 - nature.com
Identifying structural variation (SV) is essential for genome interpretation but has been
historically difficult due to limitations inherent to available genome technologies. Detection …

The third revolution in sequencing technology

EL Van Dijk, Y Jaszczyszyn, D Naquin, C Thermes - Trends in Genetics, 2018 - cell.com
Forty years ago the advent of Sanger sequencing was revolutionary as it allowed complete
genome sequences to be deciphered for the first time. A second revolution came when next …

Coming of age: ten years of next-generation sequencing technologies

S Goodwin, JD McPherson, WR McCombie - Nature reviews genetics, 2016 - nature.com
Since the completion of the human genome project in 2003, extraordinary progress has
been made in genome sequencing technologies, which has led to a decreased cost per …

metaSPAdes: a new versatile metagenomic assembler

S Nurk, D Meleshko, A Korobeynikov… - Genome …, 2017 - genome.cshlp.org
While metagenomics has emerged as a technology of choice for analyzing bacterial
populations, the assembly of metagenomic data remains challenging, thus stifling biological …

Phased diploid genome assembly with single-molecule real-time sequencing

CS Chin, P Peluso, FJ Sedlazeck, M Nattestad… - Nature …, 2016 - nature.com
While genome assembly projects have been successful in many haploid and inbred
species, the assembly of noninbred or rearranged heterozygous genomes remains a major …

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

DJ Bertioli, SB Cannon, L Froenicke, G Huang… - Nature …, 2016 - nature.com
Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes
of a total size of∼ 2.7 Gb. This makes the assembly of chromosomal pseudomolecules very …

[HTML][HTML] Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

JL Weirather, M de Cesare, Y Wang, P Piazza… - …, 2017 - ncbi.nlm.nih.gov
Background: Given the demonstrated utility of Third Generation Sequencing [Pacific
Biosciences (PacBio) and Oxford Nanopore Technologies (ONT)] long reads in many …

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

K Berlin, S Koren, CS Chin, JP Drake… - Nature …, 2015 - nature.com
Long-read, single-molecule real-time (SMRT) sequencing is routinely used to finish
microbial genomes, but available assembly methods have not scaled well to larger …

[PDF][PDF] Generations of sequencing technologies: from first to next generation

M Kchouk, JF Gibrat, M Elloumi - Biology and Medicine, 2017 - edisciplinas.usp.br
DNA sequencing process utilizes biochemical methods in order to determine the correct
order of nucleotide bases in a DNA macromolecule using sequencing machines. Ten years …