Biolite

Description

biolite website

BioLite is a bioinformatics framework written in Python/C++ that automates the collection and reporting of diagnostics, tracks provenance, and provides lightweight tools for building out customized analysis pipelines. BioLite provides generalized components aimed at developers of NGS analyses workflows. These include: * A 'catalog' database for pairing metadata with and organizing NGS data files. * A global 'diagnostics' database that establishes provenance for analyses and archives analysis results that can be accessed across multiple stages of a workflow, or from different workflows. * A modular 'pipeline' framework with Python wrappers and workflows for commonly used NGS tools, and logging, profiling, and checkpointing functionality * A C++ library 'seqio' for efficient I/O of large NGS data files it to ~/.biolite/biolite.cfg and modify for your analyses.

Environment Modules

Run module spider biolite to find out what environment modules are available for this application.

Environment Variables

• HPC_BIOLITE_DIR - installation directory
• HPC_BIOLITE_BIN - executable directory
• HPC_BIOLITE_CONF and BIOLITE_CONFIG - default configuration file. Copy

Categories

biology, genomics, variant_calling