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 develop...etecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler", https://github.com/isovic/graphm...2331 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the spe...entation of the idea of the rectangle graph approach is already included...n, we're also releasing the Rectangle Graph Module (RGM) as the separate...rrent implementation of the rectangle graph...2330 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, usi...lumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph...1992 days ago
RGFA: powerful and convenient handling of assembly graphs
RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit...near paths can be performed. A typical application of RGFA is the editing of a graph,...1577 days ago
PhyloGrapher - Graph Visualization Tool
PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs...2261 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...2203 days ago
2203 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-ge...me). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original a...exing scheme is called a Hierarchical Graph...2199 days ago
MIX: Combining multiple assemblies from NGS data
Mix is a tool that combines two or more draft assemblies, without relying on a referenc...nishing. The proposed algorithm builds an extension graph where vertices represent extr...put assembly corresponds to a path in the extension graph...2199 days ago
2193 days ago