leejheth/NGS

NGS quality control, alignment, visualization

NGS

A project as part of Swiss Institute of Bioinformatics course "NGS data quality control, alignment, visualization"

RNA-seq data analysis project.

Installation

Prerequisite: conda

Linux

conda env create -f environment.yml
conda activate ngs-tools

MacOS

conda create -n ngs-tools python=3.8
conda activate ngs-tools
conda install -y -c bioconda samtools bwa fastqc fastp sra-tools cutadapt bowtie2 hisat2 subread entrez-direct minimap2

Reference

• https://github.com/sib-swiss/NGS-introduction-training

• Singhania A, Graham CM, Gabryšová L, Moreira-Teixeira L, Stavropoulos E, Pitt JM, et al (2019). Transcriptional profiling unveils type I and II interferon networks in blood and tissues across diseases. Nat Commun. 10:1–21. https://doi.org/10.1038/s41467-019-10601-6