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