Snakemake pipelines for preprocessing of NGS Illumina short read data including RNA-seq, Whole genome sequencing and exome sequencing data
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Software packages
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Reference genomes
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RNA-seq Pipeline
run_snakemake.sh path/to/unaligned/ RNA genome_version paired_or_single_end subsample_option
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Whole Genome Sequencing Analysis Pipeline
run_snakemake.sh path/to/unaligned/ gDNA genome_version paired_or_single_end subsample_option
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Exome-Seq Pipeline
run_snakemake.sh path/to/unaligned/ Exome genome_version paired_or_single_end subsample_option