R-Toolbox for Nanopore Pipeline: Automated Analysis of cDNA Sequencing Data

This script is under construction, we are very grateful for suggestive contributions and ideas.

The pipeline was designed to integrate following tasks:

Combine fastq files from nanopore outputs, trim sequences and seperate barcoded samples, alignment and analysis

How to install the package from GitHub

Download Script from Github, required packages are:

library(DESeq2)
library(rapport)
library(RColorBrewer)
library(AutoPipe)

Also required is installed Porechop, Minimap2, Sam tools. Be sure that all tools are avaiable within your system.

The Pipeline is working steps:

# Easy Workflow for Nanopore Alignment

Samples_discription=read.csv("samp_desc.csv", row.names=1)
#Example of the sample description is given


#Set up a object from "Poreseq" class
Set=Poreseq(Samples_discription)

# path of the folder where the "fastq" folder is located
Set@path=c("path_to_file")

# Combine fastq files
GET_FASQ(Set)

# Multiplex Samples
TRIM_Barcodes(Set)

# Alignment der Sequences
Set=NANOPORE_Aligner(Set)

#Analyze Data
Set=Analyzer(Set,Write_exp=T,filter_genes=50,MA_PLOT=T)

Good luck...

Authors

D. H. Heiland, Translational Research Group, Medcal-Center Freiburg, University of Freiburg