nanoporetech/pod5-file-format

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Pod5: a high performance file format for nanopore reads.

Stars: 177
Forks: 41
Open beginner issues: 0
Indexed issues: 46

Dominant language: C++
License: No license data
Last GitHub push: Aug 24, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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46 open issues indexed

Conda packaging mismatch for POD5 and PyArrow on Python 3.12 Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nanoporetech/pod5-file-format#197 · 1 comment · Opened Sep 8, 2026
Expose AsyncSignalLoader worker count through the Python Reader API Open

Difficulty 4/5 3-5 days Newbie friendliness 68/100

nanoporetech/pod5-file-format#196 · Opened Sep 3, 2026
Enhancement: evaluate PDZ lossless compression for POD5 raw signal data Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

nanoporetech/pod5-file-format#194 · 4 comments · Opened Jun 18, 2026
problem with merging pod5 files from pod5, pod5_skip and pod5_recovered folders Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nanoporetech/pod5-file-format#192 · Opened Jun 1, 2026
Q: vbz_decompress_signal return "Input data not compressed by zstd" Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#191 · 1 comment · Opened Mar 22, 2026
Question: Infer the Sequencing Start/End Time of Each Read? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#190 · Opened Mar 10, 2026
Temp files not in work directory Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

nanoporetech/pod5-file-format#187 · 2 comments · Opened Jan 13, 2026
File is uncompressed? Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

nanoporetech/pod5-file-format#184 · Opened Nov 13, 2025
Empty path passed and invalid Read ID with pod5 view and pod5 subset Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#183 · Opened Oct 27, 2025
Feature request / question: Convert VBZ-compressed pod5 to ZSTD-compressed pod5 not supported in 0.3.34 Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#182 · 6 comments · Opened Oct 27, 2025
IOError Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#180 · 4 comments · Opened Oct 17, 2025
[POD5 merging] RuntimeError: Invalid: Unexpected empty message in IPC file format Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#178 · Opened Oct 13, 2025
POD5 has encountered an error: 'Invalid: flatbuffer size 1862616117 invalid. File offset: 9165526712, metadata length: 256' Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#176 · 2 comments · Opened Sep 15, 2025
pod5 inspect reads failures Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#175 · 2 comments · 1 reaction · Opened Sep 4, 2025
POD5 has encountered an error: 'IOError: Invalid signature in file Open

Difficulty 4/5 3-5 days Newbie friendliness 32/100

nanoporetech/pod5-file-format#173 · 8 comments · Opened Aug 22, 2025
loading signal_pa from pod5 is very slow for some files Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nanoporetech/pod5-file-format#171 · 6 comments · Opened Aug 5, 2025
Efficient python writing Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#169 · Opened Jul 10, 2025
Efficient pod5 writing code in C/C++ Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

nanoporetech/pod5-file-format#167 · Opened Jul 7, 2025
Best way to subset specific sequence ids from pod5 files Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nanoporetech/pod5-file-format#164 · 1 comment · Opened May 30, 2025
fast5 conversion crashes with free(): invalid pointer and hangs on some files Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#162 · 3 comments · Opened Apr 22, 2025
little and big endian support Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#161 · Opened Apr 16, 2025
How to get POD5 kit name? Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#160 · 1 comment · Opened Mar 11, 2025
Error in pod5 conversion Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#158 · 8 comments · Opened Feb 22, 2025
Request methods to plot signals in a specific regions Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nanoporetech/pod5-file-format#156 · 3 comments · Opened Dec 11, 2024
Discrepancy Between Parsed Read IDs and Calculated Transfers in pod5 filter Command Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#153 · Opened Nov 23, 2024
pod5 merge finished without errors at 73% Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#148 · 2 comments · Opened Oct 16, 2024
Performance issue converting fast5 -> pod5 with multiple threads Open

Difficulty 4/5 3-5 days Newbie friendliness 32/100

nanoporetech/pod5-file-format#146 · 5 comments · 1 reaction · Opened Oct 7, 2024
pod5 merge Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#145 · Opened Sep 27, 2024
Question about iteratively getting a read subset Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nanoporetech/pod5-file-format#136 · 5 comments · Opened Jul 17, 2024
Pyarrow error Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#135 · 11 comments · Opened Jul 4, 2024
Timeout Issue with POD5 conversion Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#134 · 21 comments · Opened Jun 25, 2024
pod5 merge hangs indefinitely at 99-100%(the last 20 pod5 have not been merged) Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#131 · 5 comments · Opened Jun 9, 2024
Cannot install pod5 through pip on ARM due to dependency issues Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#114 · 11 comments · Opened Feb 19, 2024
Semaphore hissy fit at the end of subset run Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#111 · 1 comment · Opened Feb 8, 2024
option to split pod5 by size/read number Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#109 · 3 comments · Opened Feb 4, 2024
Failed requirement 'flatbuffers/2.0.0@nanopore/testing' from 'conanfile.py Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

nanoporetech/pod5-file-format#101 · 3 comments · Opened Dec 18, 2023
Metadata editing in pod5 files Open

question

nanoporetech/pod5-file-format#100 · 10 comments · 1 assignee · Opened Dec 15, 2023
pod5 filter freeze Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nanoporetech/pod5-file-format#95 · 3 comments · Opened Dec 9, 2023
Q: `pod5 subset <..> --threads` takes a lot of resources Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nanoporetech/pod5-file-format#93 · 2 comments · Opened Dec 1, 2023
Pod 5 subsets Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nanoporetech/pod5-file-format#92 · 1 comment · Opened Nov 30, 2023
memory error Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nanoporetech/pod5-file-format#82 · 13 comments · Opened Oct 29, 2023
pod5 subset cannot shard a large aggregate pod5 file Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#72 · 6 comments · Opened Sep 17, 2023
pod5 convert fast5 does not gracefully exit after an error when using "strict" Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#68 · 1 comment · Opened Sep 14, 2023
pod5 don't seem to save much space on short reads Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#66 · 7 comments · Opened Aug 30, 2023
More info on some read table values Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nanoporetech/pod5-file-format#62 · 13 comments · Opened Jul 25, 2023
No pod5 conda package Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nanoporetech/pod5-file-format#36 · 16 comments · Opened May 2, 2023

nanoporetech/pod5-file-format

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