Results for "Graph Theory"
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TULIP - The Uncorrected Long read Integration Pipeline
TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as p...s as input alignments files of long reads to sparse short seeds, and outputs a graph...2191 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 pseudoknot-containing RNAs, to...h such structural feature. The bpRNA code is written in perl and requires the Graph...2184 days ago
- BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with d...
2184 days ago
- ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequenc...daries to detect transcript isoforms, which are reported as splice graphs...
2143 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads...n constructs a novel data structure called red-black multipositional de Bruijn graph...2140 days ago
FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of l...d an FM-index and use that as an implicit de Bruijn graph. Each long read is then corre...ing high frequency k-mers in the implicit de Bruijn graph....2104 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy an...reads are corrected using the short reads. Current approaches rely on various graph...2094 days ago
SeqMonk:A tool to visualise and analyse high throughput mapped sequence data
SeqMonk is a program to enable the visualisation and analysis of mapped sequence dat...a. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which...2073 days ago
VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity
VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF).2023 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows...2009 days ago
