Results for "graph"
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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....2249 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
...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...2191 days ago
- ...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 opt...
2191 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
...ence genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original a...s new indexing scheme is called a Hierarchical Graph FM index (HGFM). more...2188 days ago
MIX: Combining multiple assemblies from NGS data
...s speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extr...n. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative...2187 days ago
- ...dentification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting c...
2181 days ago
TULIP - The Uncorrected Long read Integration Pipeline
...nents 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.2180 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
..., along with the positions, sequence, and flanking base pairs of each such structural feature. The bpRNA code is written in perl and requires the Graph perl module. Several addition...2173 days ago
- ...itch is a new method for finding putative exons and constructing splice graphs using an assembled transcrip...boundaries to detect transcript isoforms, which are reported as splice graphs in dot output format....
2132 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
...nitial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositional de Bruijn graph to detect misassemblies. In a...2129 days ago
