3d-dna: 3D de novo assembly (3D DNA) pipeline
This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes...ly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise note...2313 days ago
2303 days ago
BEAP: Blast Extension and Assembly Program
The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blas...2149 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
RestrictionDigest can simulate the reference genome digestion and generate compreh...e information, please see the academic paper published online (http://www.sciencedirect.com/science/article/pii/S071734581630001X...2147 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) re...or effectively de novo assemblying large genomes. For example, on a 32-thread compute...2180 days ago
2175 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The...s by connecting genes into contiguous regions based on predicted adjacencies. Compute...2169 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
...thms used.The core algorithms and the indexing data structures (2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Hong Kong...2167 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data...nomes and deep-coverage sequencing. Quickly open and view data files on your compute...2130 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types": Reference genome-based - an assembl...using de novo approaches. This type of RNAseq is as much of an art as well as science because assembly is heavily p...2126 days ago