peterk87 / guppywuppy

Basic service wrapping PyGuppyClient talking to fast5watch

guppywuppy

Service wrapping Oxford Nanopore PyGuppyClient

• Free software: MIT license
• Documentation: https://guppywuppy.readthedocs.io.

Features

• pulls FAST5 files from a fast5watch server running on a machine running MinKNOW
• sends FAST5 files to a guppy_basecall_server for real-time GPU accelerated basecalling
• saves FASTQ files in a similar format to guppy_basecaller
• compatible with Rampart analysis and visualization

Known Issues

zmq.error.ZMQError: Too many open files

ulimit -n may be set really low (e.g. 1024) and needs to be set higher for ZMQ to be able to open a large number of sockets (see issue zeromq/jeromq#183)

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.