Musket: a multistage k-mer spectrum based corrector
...he top performing substitution-error-based correctors. In addition, Musket is multi-threaded using a master-slave model and demonstrates superior parallel scalability compared to all o...2345 days ago
MUMmer4: A fast and versatile genome alignment system
...straints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing of input query seq...2286 days ago
minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.2176 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...ionally difficult problem of assembly by breaking the reads into small, manageable subsets which can then be assembled quickly and efficiently in parallel. Applications include those i...2113 days ago
BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly...2022 days ago
pWhatsHap: a parallel, high-performance version of WhatsHap
...analysis pipelines, we have designed and engineered pWhatsHap, a parallel, high-performance version of&...ble solutions which is exponential in the coverage of the dataset. The parallel implementation on multi-core...2002 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
...orithm, based on the Disjoint Sets Data Structure, allows the computation of sequence families with low time and space requirements. A parallel version of SiLiX, based...1974 days ago
PilonGrid: parallel wrapper around the Pilon framework
The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the pipeline.1973 days ago
MSAProbs - Parallel and accurate multiple sequence alignment
...r shared-memory CPUs by employing a multi-threaded design, and further parallelized for distributed-memory sy...ms using MPI to overcome high memory overhead barrier and achieve good parallel and data-size scalability.1764 days ago
1691 days ago