NGS_Preprocessing_Pipelines

Snakemake pipelines for preprocessing of NGS Illumina short read data including RNA-seq, Whole genome sequencing and exome sequencing data

Prerequisites

• Software packages

• Reference genomes

Software Installation

Running the NGS Pipelines

• RNA-seq Pipeline

  run_snakemake.sh path/to/unaligned/ RNA genome_version paired_or_single_end subsample_option

• Whole Genome Sequencing Analysis Pipeline

  run_snakemake.sh path/to/unaligned/ gDNA genome_version paired_or_single_end subsample_option

• Exome-Seq Pipeline

  run_snakemake.sh path/to/unaligned/ Exome genome_version paired_or_single_end subsample_option

Contact

CCRSF_IFX@nih.gov