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...2099 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 both strands of a pr...2098 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.2090 days ago
MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies
...sage of available genomic resources, supports biological particulars of model organism frequently used in E&R studies and offers a wide range of different adaptive models (selective sweeps, polygenic...2061 days ago
2023 days ago
GWASpro: A High-Performance Genome-Wide Association Analysis Server
...es, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized t...1991 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
...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...1963 days ago
1956 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
...icular, it accomplishes this by: Learning locus-specific PCR stutter models using an EM algorithm...population-scale sequencing data Employing a specialized hidden Markov model to align reads to candidate a...1900 days ago
geck: trio-based comparative benchmarking of variant calls
Determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype Caller on the high-confidence SNPs of the NIST Ashkenazim trio and t...1827 days ago