JWDebler / FixFAST5

Fixing Oxford Nanopore FAST5 files which are missing entries

FixFAST5

Fixing Oxford Nanopore FAST5 files which are missing entries.

The scripts were written by HalfPhoton and provided in a github issue. I am just bringing them together here to make it easier on myself should I come accross this problem again in the future.

The scripts in this repository require pod5 tools to be installed.

Find problems in FAST5 files

python find_fast5_issues.py FOLDER_CONTAINING_FAST5_FILES/

Extract bad reads

grep -o "read_[0-9a-f-]*" issues.txt > bad_reads.txt

Delete broken entries from FAST5 files

python delete_fast5_reads.py FOLDER_CONTAINING_FAST5_FILES/ bad_reads.txt

All in one

python find_fast5_issues.py FOLDER_CONTAINING_FAST5_FILES/ && \
grep -o "read_[0-9a-f-]*" issues.txt > bad_reads.txt && \
python delete_fast5_reads.py FOLDER_CONTAINING_FAST5_FILES/ bad_reads.txt