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Adaptive sampling ReadUntil
Miles edited this page Dec 7, 2020
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| ❗ This section is under construction |
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This page will contain any information related to adaptive sampling/sequencing on using Nanopore tech on the Jetson single board computers.
As of December 3rd 2020 we can confirm that this works through the form available in the latest release of MinKnow. This has been independently confirmed on 'real-time' flow cell experiments (as opposed to playback/simulation mode).
Readfish is a software tool for selective sequencing (based on the read until API), more details here.
# ensure you have a version of python3.7 with require dev libs
sudo apt install python3.7 python3.7-dev python3.7-venv
# Make a virtual environment
python3.7 -m venv readfish
. envs/readfish/bin/activate
pip install --upgrade pip
# install required packages/wheels/libs
pip install wheel
pip install Downloads/xavier_minit_build/ont_pyguppy_client_lib-4.0.15-cp37-cp37m-linux_aarch64.whl
pip install git+https://github.com/nanoporetech/[email protected]
pip install git+https://github.com/LooseLab/readfish@dev
# check readfish is installed
readfish --versionBuilding minimap2 for arm:
git clone https://github.com/lh3/minimap2.git
cd minimap2
make arm_neon=1 aarch64=1...
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