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snakeflow

My NGS workflows based on snakemake

workflows include:

  • RNA-seq (Salmon,hisat2)
  • ChIP-seq (MACS2)
  • ATAC-seq (MACS2)
  • CITE-seq (Antibody captured, 10X genomics)
  • Germline SNV calling (GATK, BCFtools)
  • Germline Structural Variant calling
    • short-read: Speedseq + svtools
    • long-read:
      • Pacbio: ngmlr/minimap2 + sniffiles

Dependency

  • General

    • samtools, deeptools, bedtools
    • fastqc, rseqc, multiqc, fastp
    • graphviz

  • python 3

    • numpy
    • pandas
    • snakemake
    • matplotlib
    • seaborn
    • gseapy
    • macs2
    • rseqc

  • R

    • DESeq2
    • tximport
    • readr
    • pheatmap
    • ggplot2
    • ggrepel
    • clusterProfiler
    • ChIPSeeker
    • EnsDb.Hsapiens.v86

  • Variant calling

    • GATK (> 4.0)
    • BCFtools
    • Speedseq + svtools
    • minimap2
    • ngmlr
    • sniffiles

  • RNA-seq

    • hisat2, salmon
    • rMATS-turbo, rmats2sashimiplot

  • Single cell genomics

  • cellranger

Installation

Set up running environment. This config file will create a python 3.x env.

bash snakeflow-enviroment-setup.sh

usage

# Step1: activate snakemake
source activate snakeflow

# Step2: clone this repo

# Step3: copy all your fastq files into fastq dir
find . -name "*fastq.gz" | while read id; do cp $id fastq/; done;

# Step4: modify config.yml with your own paramter
# Note: put config.yml in the same dir with your snakefile.
vim  config.yml

# Step5: run snakemake with -np option. this test your ``commands`` runs without any errors.
snakemake -s salmon-tximport-deseq2-v0.2.snakefile -np

# Step6: export workflow charts
snakemake -s salmon-tximport-deseq2-v0.2.snakefile --dag | dot -Tpdf > dag.pdf

# Step7: or using the default snakemake environment you've created above.
snakemake -s salmon-tximport-deseq2-v0.1.snakefile -p -j 8