Shouji: a fast and efficient pre-alignment filter for sequence alignment
...ntly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes. We introduce Shouji, a highly parallel and accurate pre-alignment fi...1647 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
...the assembly process produce an excessive number of false positive cycles. Our solution is to search the graph in multicores shared memory parallel mode using graph decompositio...1563 days ago
Nextflow: Data-driven computational pipelines
...aptation of pipelines written in the most common scripting languages. Its fluent DSL simplifies the implementation and the deployment of complex parallel and reactive workflows on clo...1540 days ago
RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.1469 days ago
1441 days ago
SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.
...bedgraph format to annotate the generated charts. SynVisio offers different types of visualizations such as Linear Parallel plots, Hive plots, Stacked Parallel Plots and Dot plots...1439 days ago
parallelLastz: Lastz with multi-threads support.
Running Lastz (https://github.com/lastz/lastz) in parallel mode. This program is for single computer with multiple core processors. When the query file format is fasta, you can specif...1356 days ago
FastProNGS: fast preprocessing of next-generation sequencing reads
FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest.1229 days ago
PaReBrick: PArallel REarrangements and BReaks identification toolkit
...blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides d...943 days ago
Genomicus: genome browser that enables users to navigate in genomes in several dimensions
...oss different species, and chronologicaly along evolutionary time. Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all...800 days ago