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Index Gene Catalog Specifications

Process Details

  • Name: index_gene_catalog
  • Process UUID: f931eh4ykkqsrdjkph8k1ucu8vgga2
  • Process Group: Annotation

Overview

This process creates a Diamond database from filtered ORF (Open Reading Frame) sequences to enable rapid sequence similarity searches and functional annotation. The Diamond database format provides optimized performance for protein sequence alignment tasks commonly used in metagenomic and genomic annotation workflows.

This process is implemented in Bash, utilizing the Diamond bioinformatics tool for database creation.

Key Functionality

  • Database Creation: Converts FASTA-formatted protein sequences into Diamond's optimized binary database format
  • Sequence Indexing: Creates searchable indices for rapid similarity searches against the gene catalog
  • Format Optimization: Prepares sequences for high-performance alignment operations in downstream annotation processes

Input/Output Specification

Inputs

Required Inputs

  • Filtered ORF Sequences
    • Description: FASTA file containing filtered open reading frame sequences that will be indexed
    • Format: FASTA (.fasta)

Outputs

  • Diamond Database
    • Description: Binary Diamond database file containing indexed sequences for rapid similarity searches
    • Format: Diamond database (.dmnd)

Parameters & Settings

This process uses default Diamond database creation parameters and does not expose configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Diamond official documentation at https://github.com/bbuchfink/diamond
  • Related Papers: Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1), 59-60.