Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental ph...cycles. Our solution is to search the graph in multicores shared memory parallel m...1573 days ago
Nextflow: Data-driven computational pipelines
Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation.... Its fluent DSL simplifies the implementation and the deployment of complex parallel a...1550 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015...an der Auwera PDF Video 03/19/15 Mapping, processing, and duplicate marking with P...tt Sooknah PDF Video 03/19/15 Mapping and processing RNAseq Ami Levy-Moonshine P...1548 days ago
Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
Dahak is a software suite that integrates state-of-the-art open source tools for metag...ll perform various steps in metagenomic analysis workflows including data pre-processing, metagenome assembly, taxonom...1501 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.1479 days ago
1451 days ago
SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.
SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection...isio offers different types of visualizations such as Linear Parallel plots, Hive plots, Stacked Parallel P...1449 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 sp...1366 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.1240 days ago
QuasR: Quantification and annotation of short reads in R
The QuasR package (short for Quantify and annotate short reads in R) integrates the fu...ughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantifi...1010 days ago