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

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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.