some scripts used in bioinformatics research

This repo contains the pipeline and methodology as well as results of the Chip-seq analysis project

SIB course that introduces analysis of NGS data

GitHub for the SIB courses NGS - Genome variant analysis

The repository is used to calculate the NGS data sequencing read depth.

Raw code to get polymorphisms from samples analysed by using the PowerSeq® CRM Nested System kit (Promega Corporation)

linked with Bioinformatics analysis

Set of scripts to process RAD-Seq HTS data on computing grids like MetaCentrum.

Code of the article that describes the molecular epidemiology analyses of OsHV-1 virus by whole genome sequencing approaches in French shellfish growing areas.

This script takes advantage of read pairing in bam/cram files to identify the presence of STR extensions.

Bioinformatic pipeline for SARS-CoV-2 sequence analysis

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

These scripts were used to bioinformatically process the NGS data associated with the manuscript entitled "Illuminating the bacterial microbiome of Australian ticks from companion animals with next-generation sequencing", authored by Telleasha L. Greay, Kimberly L. Evasco, Megan L. Evans, Paola Magni, Una M. Ryan and Peter J. Irwin. The raw data…

Utilities for analyzing next generation sequencing data.

Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.

生物信息学项目实践仓库🏆🥇

WIP & POC: Count Viral and other non-human genome signatures in Human NGS data