Jabba: Hybrid Error Correction for Long Sequencing Reads
...(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...1982 days ago
RGFA: powerful and convenient handling of assembly graphs
RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user...near paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a...1567 days ago
PhyloGrapher - Graph Visualization Tool
PhyloGrapher is a program designed to visualize and study evolutionary...n families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements....2251 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
...lye 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...2193 days ago
2193 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignmen...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 FM index (HGFM). more...2190 days ago
MIX: Combining multiple assemblies from NGS data
Mix is a tool that combines two or more draft assemblies,...nishing. The proposed algorithm builds an extension graph where vertices represent extr...put assembly corresponds to a path in the extension graph that maximizes the cumulative...2190 days ago
2183 days ago
TULIP - The Uncorrected Long read Integration Pipeline
TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. Thes...s as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures.2182 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex p...h such structural feature. The bpRNA code is written in perl and requires the Graph perl module. Several addition...2175 days ago