BioConvert

BioConvert converts between life-science data formats to enable interoperable data transformations for alignment, sequencing, phylogeny, and variant-calling workflows.

Key Features:

• Format aggregation: Integrates existing conversion software into a unified framework and augments them with original code where necessary.
• Extensive format support: Supports approximately 50 different data formats and enables around 100 direct conversions across alignment, sequencing, phylogeny, and variant calling.
• Benchmarking and comparison: Provides a platform to benchmark and compare different conversion utilities.
• Workflow reproducibility: Standardizes format conversions to support reproducibility of data analysis workflows.

Scientific Applications:

• Alignment workflows: Converting aligner outputs and inputs between formats required by different alignment tools and downstream analyses.
• Sequencing data processing: Transforming sequencing-related file formats used across preprocessing and analysis steps.
• Phylogenetic analysis: Converting phylogeny-related formats for tree inference and downstream comparative analyses.
• Variant calling pipelines: Converting formats used in variant calling and subsequent annotation or filtering steps.

Methodology:

Aggregates existing conversion tools into a cohesive framework and augments them with custom code as needed, while providing benchmarking and comparison of conversion utilities to support reproducibility.