Usage

you MUST install snakemake following the docs and install softwares these workflows depend on.

We provide a simple way to install the dependences:

conda create env -f environment.yml  

Some dependences you need to install by your self.

Files

Files in Snakemake_codes

Snakemake_codes
|-- Nanopore_SV.py
|-- Nanopore_SV.yaml
|-- Pair-end.py
|-- Pair-end.yaml
|-- WGS.py
|-- WGS.yaml
|-- single.py
`-- single.yaml

Files ended with .py is snakemake rule for workflow running.
YAML files contains parameter settings for these workflow, defining locating of FASTQ files, reference, annotations and other setting.

Files in Data folder

Data
|-- Nanopore 
|   |-- Nano_sub
|   `-- Nano_sub.fastq.gz
|-- RNA_seq
|   |-- RNA_sub_R1.fastq.gz
|   |-- RNA_sub_R1_fastqc.html
|   |-- RNA_sub_R2.fastq.gz
|   `-- RNA_sub_R2_fastqc.html
`-- WGS
    |-- sub_R1.fastq.gz
    |-- sub_R1_fastqc.html
    |-- sub_R2.fastq.gz
    `-- sub_R2_fastqc.html

1. This Folder contains Sequencing data extract from REAL experiment sequencing reads through seqtk, these files are ending by "fastq.gz". The RNA-seq and WGS data wrere extrackted 15000 reads for every run, and 10000 reads for Nanopore sequencing.
2. The HTML file were generated by FastQC, and Nano_sub folder contains quality report generated by NanoPlot.
3. Nano_sub.fastq.gz contains a gene deletion (ZMO0028) in Zymomonas mobilis ZM4. RNA_sub_R1 and RNA_sub_R2 is paired RNA-seq data of Zymomonas mobilis 3.6M in pH6 . sub_R1 and sub_R2 is paired genome Re-seq data of Zymomonas mobilis 3.6M in pH6. (The work of strain 3.6M have been published，you can get RAW sequencing data through PRJNA590883 and PRJNA644990）

Extracted sequence is for TESTING, which contains enough reads to get data but also small enough to save uploading and running time.

Support chenyunhao@stu.hubu.edu.cn