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README.md

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GTW

Genomics training week notes and install instructions

Dependencies

WSL

This repo assumes a windows laptop with Ubuntu 20.04 LTS up an running under Windows Subsystem fro Linux WSL.

System tools

sudo apt-get install --yes gcc g++
sudo apt-get install --yes make

Flye

Flye github as key guide here

INSTALL

wget https://github.com/fenderglass/Flye/archive/refs/tags/2.9.1.tar.gz
tar -zxvf 2.9.1.tar.gz

cd Flye-2.9.1

sudo apt -y install zlib1g-dev

sudo python3 setup.py install

Kraken2

Details here

INSTALL

wget https://github.com/DerrickWood/kraken2/archive/refs/tags/v2.1.2.tar.gz
tar -zxvf v2.1.2.tar.gz
cd kraken2-2.1.2/
bash install_kraken2.sh ~/kraken2
cd ~/
sudo cp ~/kraken2/kraken2{,-build,-inspect} /usr/bin/
cd ~/krakenDB
wget -c https://refdb.s3.climb.ac.uk/kraken2-microbial/hash.k2d
wget https://refdb.s3.climb.ac.uk/kraken2-microbial/opts.k2d
wget https://refdb.s3.climb.ac.uk/kraken2-microbial/taxo.k2d

TEST DATA

wget https://github.com/fenderglass/Flye/blob/flye/flye/tests/data/ecoli_500kb_reads.fastq.gz