Analysis pipelines for genomic sequencing data

RNAseq pipeline centered on Salmon

Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

⚪ ➡️ 🔍 ℹ️ A suggested workflow, and accompanying scripts, to assemble Single Amplified Genomes (SAGs) from MDA derived Hi/MiSeq (Overlapped) Paired-End Illumina Libraries.

gwas workflow from raw intensity data to in-silico functional mapping

NGS4ECOPROD - An easy-to-use conda environment and pipelines for metagenome sequence analysis

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…

Complete Pipeline for RNA-seq data analysis: From FastQ to differntial gene expression to annotated Variations.

Pooling Illumina NextSeq 500 fastq files

GATK WGS workflow

Testing structural variant (SV) callers for illumina germline whole genome sequence (WGS) data (human).

Analysis documentation for research into the variants associated with hyperparathyroidism. Illumina, germline, human, whole exome sequence (WES) data from the CCDHB.

bash scripts used in the analysis of Illumina sequence data

Data and scripts associated with H. limbata 2014 1st instar transcriptome

A complete pipeline for assembling and analyzing the SARS-CoV-2 genome from Illumina paired-end reads, featuring quality control, mapping, variant calling, consensus sequence generation, lineage annotation, and phylogenetic analysis. Designed for efficient and modular bioinformatics workflows.

Find shared SNPs between different microarray chips

Assembly of chloroplast genome using long-reads and short-reads for Genomics Course 2021 (MSc Bioinformatics for Computational Genomics)

quality control, genome assembly, mapping for miseq, novaseq and nextseq reads