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NGS-map

A general pipeline for mapping next-gen sequencing reads and calling variants

Quick Start Instructions

Here's the rough outline of how to use these scripts to do a simple mapping analysis. The mapping analysis uses BWA, and the variant calling uses GATK.

  • Put uncompressed FASTQ file in folder data/
    • Demultiplex reads with SABRE or another such program
  • For each individual:
    • Edit variables in config.mk, especially the variables in "Paths to input files"
    • Call the individual analysis Makefile via the shell script by running sh indiv_analysis
  • When all individuals have been processed:
    • Call the comparative analysis Makefile via the shell script by running sh compare_analysis

Main Directory Structure

  • compare_analysis
    • Calls the Makefile in comparative analysis mode, to be run after all individuals have been processed.
  • config.mk
    • User-defined variables such as paths to input FASTQ files
  • data/
    • Contains FASTQ files, plus barcode data for demultiplexing [optional].
  • full_analysis.mk
    • The Makefile for the Mapping analysis. Called via sh indiv_analysis or sh compare_analysis
  • genomes/
    • Contains folders, each containing an indexed genome.
  • indiv_analysis
    • Calls the Makefile in individual analysis mode, to be run once per individual.
  • pbs/
    • Example PBS files for submitting jobs for the different parts of the analysis
  • reports/
    • Informational reports generated as the pipeline runs
  • results/
    • Output files generated as the pipeline runs
  • scripts/
    • Contains all programs needed for the pipeline.

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A general pipeline for mapping next-gen sequencing reads and calling variants

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