WIP & POC: Count Viral and other non-human genome signatures in Human NGS 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.
Utilities for analyzing next generation sequencing 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…
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
Bioinformatic pipeline for SARS-CoV-2 sequence analysis
This script takes advantage of read pairing in bam/cram files to identify the presence of STR extensions.
Code of the article that describes the molecular epidemiology analyses of OsHV-1 virus by whole genome sequencing approaches in French shellfish growing areas.
Set of scripts to process RAD-Seq HTS data on computing grids like MetaCentrum.
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
GitHub for the SIB courses NGS - Genome variant analysis
A portfolio of Nupur Upadhyay, a BS-MS student at IISER Thiruvananthapuram, Kerala, India.
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).
SIB course that introduces analysis of NGS data
Add a description, image, and links to the ngs-analysis topic page so that developers can more easily learn about it.
To associate your repository with the ngs-analysis topic, visit your repo's landing page and select "manage topics."