TULIP - The Uncorrected Long read Itegration Pipeline
...nts and/or implementations are likely to follow. Tulipseed takes as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures. Tuli...2347 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...p;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 in the GFA format....2343 days ago
2341 days ago
Bandage: interactive visualization of de novo genome assemblies
...Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can...quences. BLAST searches can be performed within the Bandage graphical user interface and the hi...2336 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-bas...2332 days ago
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
...HP genomes were proposed in the pre-NGS era and are not well suited for NGS projects. To address this limitation, we developed the first de Bruijn graph assembler, dipSPAdes, for HP...2319 days ago
Ra assembler - a de novo DNA assembler for third generation sequencing data
...an error correction step. Instead, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler", https://github.com/isovic/graphmap) and constructing and redu...2312 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
...ic implementation of the idea of the rectangle graph approach is already included...stribution, we're also releasing the Rectangle Graph Module (RGM) as the separate...om the current implementation of the rectangle graph approach in SPAdes, in the fu...2312 days ago
Jabba: Hybrid Error Correction for Long Sequencing Reads
...acBio / 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...1974 days ago
RGFA: powerful and convenient handling of assembly graphs
...eparation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a...1559 days ago