[HTML][HTML] Computational methods for chromosome-scale haplotype reconstruction

S Garg - Genome biology, 2021 - Springer
High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid
genomes, and metagenomes provide important insights into genetic variation associated …

[HTML][HTML] Towards complete and error-free genome assemblies of all vertebrate species

A Rhie, SA McCarthy, O Fedrigo, J Damas, G Formenti… - Nature, 2021 - nature.com
High-quality and complete reference genome assemblies are fundamental for the
application of genomics to biology, disease, and biodiversity conservation. However, such …

[HTML][HTML] Accurate long-read de novo assembly evaluation with Inspector

Y Chen, Y Zhang, AY Wang, M Gao, Z Chong - Genome Biology, 2021 - Springer
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 …

Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO

AA Jauhal, RD Newcomb - Molecular Ecology Resources, 2021 - Wiley Online Library
With the ever‐increasing number of publicly available eukaryotic genome assemblies and
user‐friendly bioinformatics tools, there are increasing opportunities for researchers to use …

[HTML][HTML] Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly

M Gavrielatos, K Kyriakidis… - Molecular …, 2021 - spandidos-publications.com
Genome assemblers are computational tools for de novo genome assembly, based on a
plenitude of primary sequencing data. The quality of genome assemblies is estimated by …

[HTML][HTML] The rise and fall of the ancient northern pike master sex-determining gene

Q Pan, R Feron, E Jouanno, H Darras, A Herpin… - Elife, 2021 - elifesciences.org
The understanding of the evolution of variable sex determination mechanisms across taxa
requires comparative studies among closely related species. Following the fate of a known …

[HTML][HTML] A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues

JM Ranz, PM González, BD Clifton… - Communications …, 2021 - nature.com
A detailed knowledge of gene function in the monarch butterfly is still lacking. Here we
generate a genome assembly from a Mexican nonmigratory population and used RNA-seq …

[HTML][HTML] Evaluation of a high-throughput, cost-effective Illumina library preparation kit

ES Tvedte, J Michalski, S Cheng, RS Patkus… - Scientific Reports, 2021 - nature.com
Library preparation for high-throughput sequencing applications is a critical step in
producing representative, unbiased sequencing data. The iGenomX Riptide High …

[HTML][HTML] ReSeq simulates realistic Illumina high-throughput sequencing data

S Schmeing, MD Robinson - Genome biology, 2021 - Springer
In high-throughput sequencing data, performance comparisons between computational
tools are essential for making informed decisions at each step of a project. Simulations are a …

Four Reference Quality Genome Assemblies of Pyrenophora teres f. maculata: A Resource for Studying the Barley Spot Form Net Blotch Interaction

NA Wyatt, TL Friesen - Molecular Plant-Microbe Interactions, 2021 - Am Phytopath Society
Pyrenophora teres is the causal agent of net blotch, the most devastating foliar disease of
barley. In nature, net blotch is seen in two forms, net form net blotch, caused by P. teres f …