De Novo Assembly of Plant and Animal Genomes: From Next Generation to Next-Next GenerationJiang, Wenkai
De novo assembly and analyses of 12 maize founder inbred lines (FILs) reveal abundant genetic variations among these FILs and, through expression quantitative trait loci and association analyses, we identify several SVs contributing to genomic and phenotypic differentiations of various heterotic groups. ...
Chiifu v3.0, the currentB. rapareference genome, still contains hundreds of gaps. Here, we presented a near-complete genome assembly ofB. rapaChiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultra long-read sequencing and Hi-C technologies. The ...
2020). This effectively reduces the input data and downstream processing required for the assembly of accurate and highly complete genomes, reducing the cost barrier to de novo assemblies, and making genomic tools more accessible in threatened species conservation. In Aotearoa New Zealand (hereafter ...
taxonomic annotation for each contig was given by the lowest common ancestor shared by at least 90% of the assigned genes on that contig. Assembly, binning and genome annotation After quality filtering using Sickle (Joshi and Fass, 2011), each sample was de novo assembled sepa- CAZyme ...
Metagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging to assemble from metagenomic samples due to their genomic diversi
Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. Results Sequencing data from a carrot...
Fast-Plast (https://github.com/mrmckain/Fast-Plast), NOVOPlasty [23], and ORG.asm (https://git.metabarcoding.org/org-asm/org-asm/org- asm) were proposed as fast tools to conduct de novo assembly of complete organelle genomes from WGS data. However, these tools have not been ...
Genomic assembly was performed using SMARTdenovo software (https://github.com/ruanjue/smartdenovo; parameter: -p jvh -k 17 -J 2000 -t 32 -c 1). Two rounds of error correction were performed on the assembly result based on the Nanopore sequencing data using Racon (v.1.4.11) (https:/...
GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters