make_nr

make_nr generates non-redundant FASTA files by collapsing duplicate sequences into single representative entries to prepare data for downstream sequence analyses such as NCBI BLAST+.

Key Features:

• Non-Redundancy Creation: Processes input FASTA files to identify identical sequences and collapse them into single representative entries.
• BLAST+ Integration: Produces non-redundant FASTA outputs suitable for building BLAST databases with NCBI BLAST+ tools such as makeblastdb.
• Galaxy Compatibility: Can be integrated into Galaxy workflows to preprocess FASTA inputs prior to sequence comparison and analysis.

Scientific Applications:

• Sequence Verification: Supports verification of sequencing results, including capillary sequencing, by removing duplicate sequence artefacts before comparison.
• Genome Annotation: Facilitates genome annotation by eliminating duplicate sequence entries that can confound gene prediction and annotation.
• Pan-genome Analysis: Helps manage large pan-genome datasets by collapsing identical sequences to reduce redundancy and computational load.

Methodology:

A Python script scans FASTA files, identifies duplicate sequences using sequence-comparison algorithms, and consolidates duplicates into single representative entries.