A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

A pipeline for detecting Somatic Insertion of DE novo RETROcopies

Nextflow pipeline for whole-genome sequencing (WGS) analysis and variant calling in bacterial genomes using Illumina data, supporting de novo assembly and reference-based analysis.

M.bovis WGS surveillance tool.

Call and score variants from WGS/WES of rare disease patients.

In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.

In this repository, we have compiled the WGS analysis schematics of the bacterial isolates obtained from poultry manure of layer and broiler poultry farms

A web-browser app to visualise, interpret and prioritise genomic/transcriptomic structural variations (SVs) of multiple samples.

Data management of large-scale whole-genome sequence variant calls (Development version only)

In this repository I backup the pipelines I write for the project I am involved

Shortbread2 is a bioinformatics pipeline for identifying single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from High-Throughput Next Generation Sequencing (NGS) data.

Genomic data manipulation tool

vSNP -- validate SNPs

Analysis pipelines for genomic sequencing data

El genoma pequeño - analysis workflow for "the little genome." This repository holds a computational workflow to analyze the mitochondrial genome.

A flexible metagenomic pipeline combining read-based, assemblies and MAGs with downstream analysis

vSNP -- validate SNPs

Program for positive genetic identification and IBD detection from low-coverage sequencing data

WGSL based pixel shader format that can run on native and Web.

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing