Ivan's repositories
2020-Genome_Assembly_Workshop
Explore the world of genome assembly and gain an understanding of the power and pitfalls of sequencing technologies and assembly techniques.
2020-mRNA_Seq_Workshop
Focused multi-day workshop covering the material needed for a successful RNA-Seq experiment.
assembly_improvement
Improve the quality of a denovo assembly by scaffolding and gap filling
blog
Code for personal blog. Built using blogdown and Hugo, with deployment through Netlify
centrifuge
Classifier for metagenomic sequences
datasharing
The Leek group guide to data sharing
ISEScan
A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
make_SILVA_db
General procedure for making QIIME 2 compatible SILVA reference files
MGEfinder
A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
plasmidtron
Assembling the cause of phenotypes and genotypes from NGS data
ProgrammingAssignment2
Repository for Programming Assignment 2 for R Programming on Coursera
R-graph-gallery
A website that displays hundreds of R charts
r-socialsci
Lesson on R for social scientists.
saffrontree
SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
shovill
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
srst2
Short Read Sequence Typing for Bacterial Pathogens
the-turing-way
Host repository for The Turing Way: a how to guide for reproducible data science
tormes
Making whole bacterial genome sequencing data analysis easy
vcfstats
Powerful statistics for VCF files
Workflows_and_package_management
Reproducibility and package management : workflow languages (CWL, Snakemake, Conda).