NGS pipelines Tools

This pipeline is designed for automated end-to-end quality control and processing of ATAC-seq and DNase-seq data. The pipeline can be run on compute clusters with job submission engines as well as on stand alone machines. It inherently makes uses of parallelized/distributed computing.

Augur is a bioinformatics toolkit to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines. Augur originated as part of Nextstrain, an open-source project to harness the scientific and public health potential of pathogen genome data.

Bactopia is a flexible pipeline for complete analysis of bacterial genomes.