Results for "Assembler"
Tags
Hapsembler: An Assembler for Highly Polymorphic Genomes
Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. http://compbio.cs.toronto.edu/hapsembler/Tags: Hapsembler, Assembler, Polymorphic, Genomes, Assembly, Genome
2167 days ago
- PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct contig, PERGA uses paired-end reads and differen...
Tags: PERGA, Paired-End, Read, Guided, De Novo, Assembler, Extending, Contigs, SVM, Look, Ahead, Approach, assembly
2152 days ago
- DISCO is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler. Disco was developed as a scalable assembler to assemble large metagenomes from billions of Illumina sequencing reads of complex microbial communities. Disco was parallelized for...
Tags: multiprocess, distributed, memory, overlap, layout, consensus, OLC, metagenome, assembler
2482 days ago
Ra assembler - a de novo DNA assembler for third generation sequencing data
Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in development since 2014 in the form of several separa...Tags: Ra, assembler, de novo, DNA, assembler, third, generation, sequencing, assembly
2312 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After the initial assembly, Flye performs an extra repe...Tags: Flye, de novo, assembler, ONT, Nanopore, PacBio, Assembly, single, molecule, sequencing, reads
2184 days ago
- MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. The assembly process can be summarized as follows: overlap patch reads overlap (again) scrubbing assembly graph construction and touring o...
Tags: MARVEL, assembler, Assembly, Genome, ONT, Nanopore, PacBio
2184 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be proved preserving all phasing paths from reads and p...Tags: Scallop, reference-based, transcriptome, assembler, RNA-seq, Tools
2181 days ago
Ranbow: a haplotype assembler for polyploid genomes
Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing, Ranbow utilizes the assembled haplotypes to imp...Tags: Ranbow, haplotype, assembler, polyploid, genomes, Assembly, NGS
2156 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, thos...Tags: PRICE, Paired-Read, Iterative, Contig, Extension, de novo, genome, assembler, C++.
2147 days ago
BASE: a practical de novo assembler for large genomes using long NGS reads
new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use revers...Tags: BASE, practical, de novo, assembler, large, genomes, long, NGS, reads
2016 days ago
