MIX: Combining multiple assemblies from NGS data
...s speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extr...2204 days ago
HALC: High throughput algorithm for long read error correction
...roach) HALC was able to obtain 6.7-41.1% higher throughput than the existing algorithms while maintaining...reads can thus result in 11.4-60.7% longer assembled contigs than the existing algorithms....2173 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
...+. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those con...2170 days ago
mScaffolder: A comparative genome scaffolding tool
A comparative genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer uti...2166 days ago
CGView - Circular Genome Viewer
...g, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases...2161 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...n run as a stand-alone app on OSX and Windows using the Electron platform Highly extensible plugin architecture, with a large plugin registry of existing examples here https://gmod.gi...2152 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...cal assembly of unmapped mates of mapped short reads. Our results on bacterial, fungal and insect data sets show that CoLoRMap compares well with existing hybrid correction methods.The...2099 days ago
SimLoRD: A read simulator for third generation sequencing reads
...ater stage.) The read lengths can be determined in four ways: drawing from a log-normal distribution (typical for genomic DNA), sampling from an existing FASTQ file (typical for RNA),...2098 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
.... The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides another practical alternative to existing mate-pair_based approaches or...2082 days ago
funannotate: Eukaryotic Genome Annotation Pipeline
...e larger genomes. The impetus for this software package was to be able to accurately and easily annotate a genome for submission to NCBI GenBank. Existing tools (such as Maker) require...2070 days ago