Pinned Repositories
2023_drosophila_assembly
Genome assembly pipelines used in Kim et al. 2023
chipster
Chipster is a user-friendly analysis software for high-throughput data.
Culturome
geocompr
Open source book: Geocomputation with R
lab-docs
The Ross-Ibarra's lab documentation
long-read_SV_calling
Snakemake pipelne to call structural variants from long-read DNA sequencing
LongRead_tutorials
Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
MASS_validation_source_code
Input data and R script for validating marker-assisted seedling selection efficiency in an apple seedling population
StatisticalMethodsforOmicsAssistedBreeding
Slides for short course on 'omics assisted breeding methods
Sultan-Mia's Repositories
Sultan-Mia/long-read_SV_calling
Snakemake pipelne to call structural variants from long-read DNA sequencing
Sultan-Mia/2023_drosophila_assembly
Genome assembly pipelines used in Kim et al. 2023
Sultan-Mia/agridat_agricultural-experimental-dataset
Agricultural datasets
Sultan-Mia/Air_Metagenomics
This repository focuses on the metagenomic analysis of bioaerosols using nanopore sequencing. It highlights our use of nanopore's R10 chemistry for its high accuracy and throughput, alongside the Rapid Barcoding Kit 114 for streamlined sample preparation.
Sultan-Mia/bacterial-genomics-tutorial
All recipies
Sultan-Mia/Bioinformatics_Tutorials
Bioinf Tutorials
Sultan-Mia/Counting-crop-grains-with-pliman
Sultan-Mia/denbi-nanopore-training
de.NBI Nanopore Training Course
Sultan-Mia/DSFAIR_Data-Science-for-Agriculture-in-R
:bar_chart::seedling: Data Science for Agriculture in R
Sultan-Mia/dsfair_quarto_Agricultural_Statistics-in-R
under construction
Sultan-Mia/Guppy_Basecaller
GPU basecalling
Sultan-Mia/guppy_parameter_optimiser
A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
Sultan-Mia/hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Sultan-Mia/Intro-to-rnaseq-hpc-salmon-flipped
Introduction to bulk RNA-seq
Sultan-Mia/Kaya-ListerLab-Tutorial
Info about how to setup, use and work on UWA's Kaya system. Includes a tutorial with example code
Sultan-Mia/Leaf-shape-analysis-with-pliman
Sultan-Mia/mag
Assembly and binning of metagenomes
Sultan-Mia/metagenomics-workshop
Sultan-Mia/mfusca_figs
Malus
Sultan-Mia/ONT-shotgun-metagenomics
The analysis of shotgun metagenomic sequencing data generated from Oxford Nanopore Technology (ONT).
Sultan-Mia/pb-human-wgs-workflow-snakemake
Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
Sultan-Mia/Pepper_T2T
Here, we report telomere-to-telomere (T2T) gap-free genomes for domesticated pepper Capsicum annuum and wild relative Capsicum rhomboideum.
Sultan-Mia/Phytopatometry-in-R-with-the-package-pliman
Sultan-Mia/shinyCircos-V2.0
an R/Shiny application for interactive creation of Circos plot
Sultan-Mia/SIMER-data-Simulation-for-genetics
Data Simulation for Life Science and Breeding
Sultan-Mia/Sniffles
Structural variation caller using third generation sequencing
Sultan-Mia/strainy
Graph-based assembly phasing
Sultan-Mia/SVbyEye
Structural variation view tool
Sultan-Mia/toulligQC-Nanopore-QC-
A post sequencing QC tool for Oxford Nanopore sequencers
Sultan-Mia/Watermelon-pangenome