Dr. Sultan Mia's repositories
LongRead_tutorials
Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
abc-phenomics
Phenotypic analysis of 1119 apple accessions within the ABC.
agridat_agricultural-experimental-dataset
Agricultural datasets
bacterial-genomics-tutorial
All recipies
bioruby-polyploid-tools
Library and tools to deal with polyploid genomics
bookdown-demo
A minimal book example using bookdown
cider-vs-dessert
This repository contains data and scripts used to repoduce analyses in the manuscript "Quantifying the differences between cider and dessert apples".
common_analyses
Repository of common bioinformatics scripts
CV
My curriculum vitae.
DSFAIR_Data-Science-for-Agriculture-in-R
:bar_chart::seedling: Data Science for Agriculture in R
dsfair_quarto_Agricultural_Statistics-in-R
under construction
GPU-accelerated-guppy-basecalling
GPU-accelerated guppy basecalling and demultiplexing on Linux
Guppy_Basecaller
GPU basecalling
guppy_parameter_optimiser
A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
Intro-to-rnaseq-hpc-salmon-flipped
Introduction to bulk RNA-seq
learning-resource-links
An awesome list of learning resources for bioinformatics, genomics and computational biology
mfusca_figs
Malus
minimalmarkers
Code for choosing the minimal set of genetic markers needed to differentiate all samples in a genotyping dataset
pb-human-wgs-workflow-snakemake
Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
PyBSASeq
A novel algorithm for BSA-Seq data analysis
Rnotebook_Self-incompatibility
Apple S-allele
shell-genomics
Introduction to the Command Line for Genomics
snphub
A Shiny-based server framework for retrieving, analyzing and visualizing the large genomic variations data in a lab.
SOAPnuke
A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files