生物信息学项目实践仓库🏆🥇

SIB course that introduces analysis of NGS data

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

GitHub for the SIB courses NGS - Genome variant analysis

Utilities for analyzing next generation sequencing data.

Bioinformatic pipeline for SARS-CoV-2 sequence analysis

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

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

Developed a Bash-based pipeline for bacterial NGS data analysis, including QC, trimming, alignment, variant calling, and annotation (FastQC, Trimmomatic, BWA, Samtools, bcftools, SnpEff).

A portfolio of Nupur Upadhyay, a BS-MS student at IISER Thiruvananthapuram, Kerala, India.

2024 DIGI+ Talent跨域數位人才加速躍升計畫

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

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

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

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…

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

linked with Bioinformatics analysis

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.

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