miniasm: very fast OLC-based de novo assembler for noisy long reads
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph...2363 days ago
2361 days ago
Bandage: interactive visualization of de novo genome assemblies
Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific are.... BLAST searches can be performed within the Bandage graphi...2356 days ago
Mugsy: multiple whole genome alignment tool
Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive mu...2352 days ago
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of hig...for NGS projects. To address this limitation, we developed the first de Bruijn graph...2340 days ago
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions
TRRUST contains 8,444 and 6,552 TF-target regulatory relationships of 800 human TFs...elationships from over 20 million pubmed articles, we used sentence-based text mining approach. TRRUST database al...2339 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 develop...etecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler", https://github.com/isovic/graphm...2333 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...2332 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...1994 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,...1579 days ago