Variant annotation and filtration server ALAPY Genome Explorer

bcftools singularity container

GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.

A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)

convert genotype array output into annotated IBD segments

Calling SNPs using TASSEL GBS V2 pipeline for ponderosa pine using the reference genome of loblolly pine

Scripts used on a cluster that demonstrate vcf file manipulation and preparation.

A bash script based pipeline to analyze Rad-seq data to get SNPs.

Script to infer the reference genome from a VCF

Built around the vcf2tsv software. Make a tsv from a vcf for the excel lovers in your life.

Bash scripts for fastq to vcf pipeline, written for USyd Artemis HPC.

Syntax highlighting for computational biology

A guide to manipulating genotypic data across the common formats: VCF, EIGENSTRAT and PLINK (PACKEDPED) files. Includes how to convert between formats, merge datasets or subset by individuals in each of the formats.

Multi-class classification of drug resistance in MTB clinical isolates

Multi-class classification of drug resistance in MTB clinical isolates

Pipeline for automated genomic variant analysis in inherited diseases, integrating alignment, variant calling, and quality control

A Bioinformatics pipeline to process Raw reads to VCF files in Bash

Convert VCF files with AF (e.g., ToMMo/jMorp, gnomAD) to ANNOVAR database format.

A collection of scripts for filtering annotated variant call format files