Albacore HowTo

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Installing on Ubuntu 16.04

$ sudo apt-get update
$ sudo apt-get install wget
$ wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add -
$ echo "deb http://mirror.oxfordnanoportal.com/apt trusty-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list
$ sudo apt-get update
$ sudo dpkg -i path/to/python3-ont-albacore-xxx.deb
$ sudo apt-get -f install

Basecalling

#!/bin/bash

FLOWCELL="FLO-MIN107"
KIT="SQK-LSK108"
NUM_THREADS=7
INPUT_DIR="./fast5"
OUTPUT_DIR="./fastq"

read_fast5_basecaller.py --flowcell $FLOWCELL --kit $KIT -o fastq \
        --worker_threads $NUM_THREADS \
        --input $INPUT_DIR -r --save_path $OUTPUT_DIR

References