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...2207 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 genom...minimap2 -a MT-human.mmi test/MT-orang.fa > test.sam # use presets (no test data)...2202 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 databa...2202 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 through all fastq files in a folder and then...results of each fastq file/pair. Currently it supports processing data f...2194 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaSc...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 a...2193 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms, it is feasibl...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....2189 days ago
2189 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...ort reads to both the contigs and reference genome, and then constructs a novel data s...2186 days ago
ASAR: Advanced metagenomic Sequence Analysis in R
An interactive data analysis tool for selection, aggregation and visualization of metagenomic data i...2183 days ago
Epiviz: an interactive visualization tool for functional genomics data.
Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other gen...owsers, but allows multiple visualizations of data within genomic regions using...ser-supplied visualizations. It also includes data f...2183 days ago