2153 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms...t is feasible to study entire transcriptomes of non-model organisms. While algorithms a...algorithm for de novo transcriptome assembly of non-model organisms. BMC Genomics 18(Su...2125 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types": Reference genome-based - an assemb...reconstruct transcripts. This category would obviously include humans and most model organisms but excludes the ma...2125 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...We designed and developed Hercules, the first machine learning-based long read error correction algorithm. The algorithm models every long read as a profile Hidden Markov Model with respect to the underlyin...2077 days ago
SimLoRD: A read simulator for third generation sequencing reads
SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from bo...2075 days ago
STELLAR: fast and exact local alignments
STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar.2068 days ago
MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies
MimicrEE2, a multi-threaded Java program for genome-wide f...nomic resources, supports biological particulars of model organism frequently used in E...udies and offers a wide range of different adaptive models (selective sweeps, polygenic...2038 days ago
2000 days ago
GWASpro: A High-Performance Genome-Wide Association Analysis Server
GWASpro supports building complex design matrices, by which complex experimental desi...ons, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized t...1968 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
...number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling metho...1940 days ago