bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable descripti...2235 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
...benefitted in time 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 developed by...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...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 geno...inimap2 -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 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 databases...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 through all fastq files in a folder and the...results of each fastq file/pair. Currently it supports processing data from...2198 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaS...ipt and HTML5, with optional run-once data formatting tools written in P...ge sequencing. Quickly open and view data files on your computer withou...d more. BAM, BigBed, BigWig, and VCF data are...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 feasib...embly 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...2194 days ago
2194 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
...reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositio...2191 days ago