Nadia Baig's Projects
Scripts of Garrido-Oter et. al, Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia
Plant genome assembly and annotation pipeline using snakemake
This repo includes ChatGPT prompt curation to use ChatGPT better. Newly added features includes Bioinformatics relevant tasks
Bioinformatics one liners from Ming Tang
Bioinfomatics algorithms in C++
📊 Circular and Rectangular Manhattan Plot
Make Complex Heatmaps
CoSSA (Prodhomme et al., 2019) is a set of workflows used to identify quickly and efficiently haplotype specific SNPs linked to a trait of interest from Whole Genome Sequencing data. All the contributors to the design of these workflows are Danny Esselink, Charlotte Prodhomme and Theo Borm (Wageningen University UR Plant Breeding).
Bash and python scripts for COSSA analysis of a test data for potato clones
The pipeline for amplicon sequencing analysis based mainly on DADA2.
A bash script based pipeline to analyze Rad-seq data to get SNPs.
A tool for reconstructing haplotypes polyploid genome using linked reads (10X Genomics).
The repository contains script and notebook related to Statistics, Machine learning, Neural network, Deep learning, NLP, Numerical methods, and Automation.
Finally learning AWK instead of being annoyed at its syntax
Config files for my GitHub profile.
Not fully functional at the moment. Code needs major changes
The set of NGS processing pipelines used at Babraham
Recipes for using Python's pandas library
Chromosome-scale and haplotype-resolved assmebly of tetraploid cultiavetd potato with polyploidy graph binning
Deep Learning (with PyTorch)
Scripts of Garrido-Oter et. al, Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia
This repository consists of short python/bash scripts that you need at some point of your NGS data processing and analysis.
Training requirements for joining projects
Bash pipeline for Single Nucleotide Polymorphism (SNP) and CNV detection in WGS data
Python and R based scripts to plot your VCF, SNP and NGS data
Short scripts for fetching nucleotide (FASTA), SRA (fastq), protein/gene information and Publication records from NCBI database for Solanum_Hugassii. Scripts can be modified to extract information for other species too.