HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

SNP genotyping in polyploids

Tools for analyzing raw DNA test data files. Shows Y chromosome and mitochondrial mtDNA haplogroups. LGPLv3 - use freely but share improvements.

Ancestry inference with convolutional neural networks

SNP and variant calling pipeline for bacteria

This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data

Convert mpileup format to base count tsv table

GWAS third-level epistatic search tool for cluster architectures

Variant calling + processing pipline using GATK based in Snakemake

DNA explorer - app for observing decrypted DNA-chains in digital format, app show information about single nucleotide polymorphisms, and provide a brief describtion - it may helps to determine if you have certain genetic predisposition to diseases, and show hidden information encoded in your DNA (your ancestries, phenotypes, predisposition to sp…

Wheat BRIL database created using FLASK server side, angularjs is heavily used at front end

SNP pipeline using Snakemake for the Weisrock Lab's Tiger Salamander project.

Workflow to perform a Variant Calling Analysis

Advanced Computational Biology Project Assignment

Population genetic analyses of seeded and wild populations of Texas bluebonnet (Lupinus texensis).

Custom scripts and workflows used in the genomics and population analysis of oat crown rust (Puccinia coronata f. sp. avenae) preprint (bioRxiv 2023.09.18.557855). All steps performed in Linux environment or R.

SARS-CoV-2 early outbreak analysis. Two polymorphism sites 8517 and 27641 (CDS numbering) were found to genotype the early strains.

SNPware is a family of short bash scripts that allows to translate genotypes coded as GCTA or Illuimina Top Strand to AB coding using standard Illumina FinalReport files to create a library of genotype equivalences at each locus.

Bioinformatics Pipeline for dRADseq Data