poredb

Poredb is a way to manage very large Oxford Nanopore datasets on the basic principle:

-- track the files, rather than moving them around

Usage

Create a DB

poredb create myexperiment.db
find . -name "*.fast5" > filelist.txt
poredb import myexperiment.db filelist.txt

Extract all basecalls in FASTQ format

poredb fastq myexperiment.db > myexperiment.fastq

Thanks

Andreas Klosterman for dask suggestion.