HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, des...variants. If you use HapCUT2 in your research, please cite: Edge, P., Bafna, V. &...2243 days ago
2243 days ago
chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
Provides interactive, configurable and elegant graphics visualization of the chromosomes or chrom...iz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data...1911 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide A...ed in time and space efficiency by a revolution in the basic data struct...res and algorithms used.The core algorithms and the indexing data...2235 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 origi...methods used for scaffolding. Ghurye, J., Pop, M., Koren, S., Bickhart, D., &...2212 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 genome ./...nimap2 -a MT-human.mmi test/MT-orang.fa > test.sam # use presets (no test data)...2207 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable map...eb browser, allowing rapid genome browsing, and facilitating data sharin...View maps to be integrated with existing web site content or datab...2207 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data After...s of each fastq file/pair. Currently it supports processing data...2198 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built comp...ith JavaScript and HTML5, with optional run-once data...deep-coverage sequencing. Quickly open and view data files...), REST, and more. BAM, BigBed, BigWig, and VCF data...2198 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non...om high-throughput sequencing data,...g their applications to small data sets with few libraries. Texas A&M Univ...tain hundreds of gigabases of data. New techniques are developed...2194 days ago