Bioinformatics pipeline

Introduction

An effective, reproducible and reliable data analysis workflow is based on the state-of-the-art pipeline, using the most up-to-date methods. In order to facilitate my future work, building the bioinformatics pipeline is necessary. However, how to construct the workflow is still hard for me. In my view, I wanna use the nextflow or snakemake program language to do it. Before doing it, what I need is to describe the workflows in the mindmap which could make me be clear.

Interests

• amplicon sequencing analysis
• metagenomics sequencing analysis
• bulk-RNA sequencing analysis
• DNA methylation by Illumina Array

Workflow

The workflow comprises of two parts, one is from raw data to profile, and the other is data analysis (statistical analysis)

• the first parts
  • demultiplex sequences;
  • scan the quality of reads;
  • filter the low quality reads and remove host DNA sequence
  • align the high quality reads into the reference database
  • obtain the profile whose structure is $M x N$ matrix (M: features’ name; N: sampleid)
• the second part
  • statistical analysis such as wilcoxon rank sum test, LDA, PCoA, linear regression analysis and multivariables association analysis
  • machine learning

Notice

First and foremost, I utilize the perl program language to do some preliminary work and finally convert all the workflows into snakemake or nextflow.