LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including...2242 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence read...and accuracy across diverse sequencing technologies, including but not limited to: NGS shor...2241 days ago
2241 days ago
chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions of..."chromosome heatmap" that, in addition to mapping elements, can visualize the data ass...1909 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...ten in perl and requires the Graph perl module. Several additional scripts for analysis are included. The source code...2233 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an update...ficiency by a revolution in the basic data structures and algorithms use....The core algorithms and the indexing data structures (2way-BWT) are develop...2233 days ago
2228 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can b...2210 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference geno...inimap2 -a MT-human.mmi test/MT-orang.fa > test.sam # use presets (no test data) ....2205 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular genome...r, allowing rapid genome browsing, and facilitating data sharing. The feature labels i...to be integrated with existing web site content or database...2205 days ago