Results for "Genome"
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Meraculous: De Novo Genome Assembly with Short Paired-End Reads
We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, wi...Tags: Meraculous, De Novo, Genome, Assembly, Short, Paired-End, Reads
2429 days ago
What are the best approach that gave good results in genome projects?
I am working on genome assembly, but wordering the optimised method to achieve the best result. Your comments and suggestions are welcome.Tags: Approach, Results, Genome, Projects, NGS, Assembly
2429 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make...Tags: Oxford, Nanopore, Sequencing, Hybrid, Error, Correction, de novo, Assembly, Eukaryotic, Genome
2407 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the specific implementation of the idea of the rectangle graph approach is already included into the current SPAdes distribution, we're also releasing the Rectangle Graph Module (RGM) as the separate code which can be run inde...Tags: Rectangle, Graph, Repeat, Resolution, Genome, Assembly
2378 days ago
- Interested in understanding the evolution of life. To obtain glimpses of such understanding, we employ existing and new methods of computational biology to perform research in several major areas. https://www.ncbi.nlm.nih.gov/research/groups/koonin/
Tags: Eugene V. Koonin, NCBI, Koonin, Evolution, Genome, Bioinformatics
2366 days ago
MeDuSa: a multi-draft based scaffolder
MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalises the scaffolding problem by means of a co...Tags: MeDuSa, multi-draft, scaffolder, NGS, Genome, Assembly
2330 days ago
funannotate: Eukaryotic Genome Annotation Pipeline
Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this software package was to be able to accurately and ...Tags: funannotate, Eukaryotic, Genome, Annotation, Pipeline
2113 days ago
Genome assembly stats plotting
A de novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length Number of scaffolds/contigs Length of longest scaffold/contig Scaffold/contig N50 and N90Assembly base composition, in particular percentage GC and percentage Ns CEGMA complet...Tags: Genome, assembly, stats, plotting
2316 days ago
