chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
Provides interactive, configurable and elegant graphics visualization of the chromo...e "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome el...1911 days ago
Hapsembler: An Assembler for Highly Polymorphic Genomes
Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. http://compbio.cs.toronto.edu/hapsembler/2236 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
SOAPaligner/soap2 is a member of the SOAP (Short Oligonu...me and space efficiency by a revolution in the basic data structures and algorithms used.The core algorithms and the indexing data structures (2way-BWT) are dev...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 original SALSA algorithm. If you want to use the old version, it can be found in th...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 sequ...minimap2 -a MT-human.mmi test/MT-orang.fa > test.sam # use presets (no test data) ./minimap2 -ax map-pb ref.f...2207 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zo...er, allowing rapid genome browsing, and facilitating data sharing. The feature labels i...s to be integrated with existing web site content or databases. For examples of the var...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 AfterQC can simply go throug...h fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/400...2198 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome brows...ript and HTML5, with optional run-once data formatting tools written in P...age sequencing. Quickly open and view data files on your computer withou...nd more. BAM, BigBed, BigWig, and VCF data are displayed directly from c...2198 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo ass...sembly from high-throughput sequencing data, they are very memory-intensi..., limiting their applications to small data sets with few libraries. T...that contain hundreds of gigabases of data. New techniques are developed...2194 days ago
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