Results for "sequencing"
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GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which combines contig order, distance and orientation...Tags: GRASS, Generic, Algorithm, Scaffolding, NGS, Sequencing, Assemblies
2529 days ago
SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also ...Tags: SIMBA, Web, Tool, Bacterial, Genome, Assembly, Ion PGM, Sequencing
2529 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file. Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets...Tags: Grinder, Biogrinder, Versatile, Omics, Shotgun, Amplicon, Sequencing, Read, simulator
2528 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric sources of noise that may be pres...Tags: simNGS, simLibrary, Software, Simulating, Next-Gen, Sequencing, Simulation
2340 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
2339 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes pr...Tags: MetaSim, Sequencing, Simulator, Genomics, Metagenomics
2334 days ago
Jabba: Hybrid Error Correction for Long Sequencing Reads
Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph should appear in fasta format with 1 entry per node...Tags: Jabba, Hybrid, Error, Correction, Long, Sequencing, Reads
1971 days ago
- The central goal of the Earth BioGenome Project is to understand the evolution and organization of life on our planet by sequencing and functionally annotating the genomes of 1.5 million known species of eukaryotes, a massive group that includes plants, animals, fungi and other organisms whose ce...
Tags: Earth, BioGenome, Project, Genome, Sequencing
2192 days ago
What are the best software options available for nanopore (ONT) reads ?
Tags: ONT, Nanopore, Assembly, Sequencing, Reads, fast
2182 days ago
