slow5-template-x

This is a template repository is mostly for my own use, but also demonstrates the advanced use of slow5lib. Documentation and comments are thus minimal and code is not so clean. For a simpler example visit slow5-template.

Compilation and running

sudo apt-get install zlib1g-dev   #install zlib development libraries
git clone --recursive https://github.com/hasindu2008/slow5-template-x
cd slow5-template-x
make
./xyztool subtool1 test/example.blow5

The commands to install zlib development libraries on some popular distributions:

On Debian/Ubuntu : sudo apt-get install zlib1g-dev
On Fedora/CentOS : sudo dnf/yum install zlib-devel
On OS X : brew install zlib

Acknowledgement

Code snippets have been taken from Minimap2.

Walkthrough

The repository contains the following:

1. slow5lib as a git submodule
2. A Makefile
3. C programmesource files
4. shell script for testing
5. GitHub actions workflow
6. Miscellaneous files such as license, .gitignore, etc

Links

SLOW5 specification: https://hasindu2008.github.io/slow5specs
slow5lib: https://hasindu2008.github.io/slow5lib/
slow5tools: https://hasindu2008.github.io/slow5tools
Pre-print: https://www.biorxiv.org/content/10.1101/2021.06.29.450255v1
Publication: https://www.nature.com/articles/s41587-021-01147-4