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amoebae

Script toolkit for identifying and classifying homologous gene/protein sequences

basic_bioinfor_scripts

Basic Scripts for Day to Day Bioinformatics

bonsai

Bonsai: Fast, flexible taxonomic analysis and classification

bowtie2

A fast and sensitive gapped read aligner

bulk-rnaseq

This repo contains scripts and workflows for performing bulk transcriptomics analyses

chatgpt

This folder contains Q&A sessions and recommendations from ChatGPT for various bioinformatics, genomics, machine-learning, coding-related tasks, and general biology inquiries. Kept as general-purpose notebook.

common_commands

de-novo-genome-assembly

Scripts for genome assembly associated tasks - scripts and parameters set up for run on Compute Canada HPC

ds-ml-day1

Python for Data Science and Machine Learning: day 1

ds-ml-day2

ds-ml-day3

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

gwas-pipeline

This is a general (somewhat comprehensive) description of the LNG GWAS pipeline which can be used to guide researchers on how-to run a GWAS.

gwas-scripts

Bash scripts provided here to run various GWAS QC, Imputation, PCA, and association testing steps using PLINK, SMARTPCA, RStats and Visualization

helpful_commands

Command-line tools, commands, and code snippets for performing routine data processing and bioinformatics tasks

jellyfish

A fast multi-threaded k-mer counter

kingfisher-download

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

kraken2

The second version of the Kraken taxonomic sequence classification system

krakentools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

krona

Interactively explore metagenomes and more from a web browser.

liftoff

An accurate GFF3/GTF lift over pipeline

machinelearning_notes

Machine learning and deep learning resources

masurca

mock-microbial-community

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

python_dsml

course material from EPFL L&D's Python for Data Sciences and Machine Learning Course (Sep 21-23)

quast

Genome assembly evaluation tool

r-stats

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

scanpy

Single-cell analysis in Python. Scales to >1M cells.