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Check Chrom Sizes And Index Specifications

Process Details

  • Name: Check_chrom_sizes_and_index
  • Process UUID: 17fc7900-e169-11e9-be30-e0aab38271b1
  • Process Group: File Conversions

Overview

This process converts FASTA genome files to chromosome sizes format and creates index files necessary for downstream genomic analyses. It generates a chromosome sizes file (.chrom.sizes) that contains the length of each chromosome or contig in the reference genome, which is essential for many bioinformatics tools and visualization applications.

This process is implemented in Bash.

Key Functionality

  • FASTA Parsing: Extracts chromosome names and calculates their lengths from FASTA sequence files
  • File Format Conversion: Converts FASTA format to tab-delimited chromosome sizes format
  • Index Generation: Creates necessary index files for genome reference usage
  • File Management: Handles existing chromosome sizes files and directory structure creation

Input/Output Specification

Inputs

Required Inputs

  • Genome
    • Description: Reference genome sequence in FASTA format
    • Format: FASTA (.fasta, .fa)

Outputs

  • Genome Sizes
    • Description: Tab-delimited file containing chromosome names and their corresponding lengths
    • Format: Sizes (.sizes, .chrom.sizes)

Parameters & Settings

This process uses internal parameters configured at the pipeline level and does not expose user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on the chromosome sizes generation script