Nextflow: Data-driven computational pipelines
Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting lang...1564 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 20...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...1562 days ago
U-Plot: Genome U-Plot sample implementation
The Genome U-Plot is a JavaScript tool to visualize Chromosomal abnormalities in the Human Genome using a U-shape layout.1552 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 me...ll perform various steps in metagenomic analysis workflows including data pre-processing, metagenome assembly, taxonom...1515 days ago
flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizati...y adding information on sequence annotations and sequence similarities to the images. Co...1500 days ago
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the...1180 days ago
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pggb: the pangenome graph builder
This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to build a graph that is l...1357 days ago
Platypus – R package for object detection and image segmentation.
platypus is an R package for object detection and semantic segmentation. Currently using platypus you can perform: multi-class semantic segmentation u...1301 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.1254 days ago