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Check Build Hisat2 Index Specifications

Process Details

  • Name: Check_Build_Hisat2_Index
  • Process UUID: 17fc79be-e169-11e9-be30-e0aab38271b1
  • Process Group: Index

Overview

This process builds a HISAT2 index using the provided genome FASTA file and GTF file. It extracts splice sites and exons from the GTF file, creates the HISAT2 index in a designated directory, and establishes a symbolic link to the index directory if it already exists. The process is designed to efficiently manage HISAT2 index creation for RNA-seq alignment workflows.

This process is implemented in Bash, which invokes Python scripts for splice site and exon extraction from GTF files.

Key Functionality

  • Index Construction: Builds HISAT2 alignment index from genome FASTA and GTF annotation files
  • Splice Site Extraction: Extracts splice sites from GTF file using HISAT2's Python utility scripts
  • Exon Extraction: Extracts exon information from GTF file to improve alignment accuracy
  • Index Management: Creates symbolic links to existing index directories when available

Input/Output Specification

Inputs

Required Inputs

  • Genome

    • Description: Reference genome sequence in FASTA format
    • Format: FASTA

  • GTF File Path

    • Description: Gene annotation file containing transcript and exon information
    • Format: GTF

Outputs

  • HISAT2 Index
    • Description: Complete HISAT2 index files for genome alignment
    • Format: Index

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Hisat2 Build Parameters
    • Description: Hisat2 build parameters
    • Default value: -p 5

References & Resources

  • Tool Documentation: Contact the team for details on hisat2_extract_splice_sites.py and hisat2_extract_exons.py
  • Related Papers: Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019). https://doi.org/10.1038/s41587-019-0201-4