changename

changename modifies chromosome or gene names in single FASTA, GFF, and SAM files to standardize nomenclature while preserving the underlying file structure and content and without support for multi-chromosome or multi-gene files.

Key Features:

• File Format Compatibility: Operates on single FASTA, GFF, and SAM file formats used for sequences, annotations, and alignments.
• Nomenclature Update: Replaces chromosome or gene names with user-specified alternatives.
• Preserves Data Structure: Maintains sequence, annotation, and alignment content while changing identifiers.
• Single-file Restriction: Limited to single-chromosome or single-gene files and does not support multi-chromosome or multi-gene inputs.
• Consistent Reference Updating: Updates all references within the file to maintain internal consistency.

Scientific Applications:

• Data Consistency: Ensures datasets adhere to updated naming conventions for accurate interpretation and cross-study comparison.
• Reproducibility: Standardizes nomenclature across datasets to support reproducible analyses and reporting.
• Workflow Integration: Can be incorporated into larger bioinformatics workflows and pipelines, for example Galaxy-based pipelines.

Methodology:

changename parses the input FASTA, GFF, or SAM file and replaces existing chromosome or gene names with user-defined alternatives, updating all internal references while preserving file content; the process is automated.