Owner

nanoporetech

6 indexed repositories · View on GitHub

dorado
Oxford Nanopore's Basecaller

C++ · 875 stars
pod5-file-format
Pod5: a high performance file format for nanopore reads.

C++ · 177 stars
rerio
Research release basecalling models and configurations

Python · 121 stars
pomoxis
Analysis components from Oxford Nanopore Research

Python · 99 stars
minknow_api
Protobuf and gRPC specifications for the MinKNOW API

Python · 73 stars
hatch-protobuf
Hatch plugin for generating Python files from Protocol Buffers .proto files

Python · 14 stars

Beginner friendly Everything

Open All

minknowd persistently binds to port 8000 on boot, causing port collisions with standard web development servers Open

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

nanoporetech/minknow_api#95 · Opened Sep 17, 2026
Support for fast5 files Open

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

nanoporetech/dorado#1633 · 1 comment · Opened Sep 14, 2026
dorado demux emit-fastq outputs all alignments Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

nanoporetech/dorado#1632 · 1 comment · Opened Sep 9, 2026
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
Docker image size and model-directory handling (DRD_MODELS_PATH) Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

nanoporetech/dorado#1630 · 4 comments · Opened Aug 27, 2026
Issue with new dorado version dorado-2.1.1 giving error std::bad_alloc Open

mods

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

nanoporetech/dorado#1624 · 3 comments · Opened Aug 17, 2026
Adapter trimming in duplex basecalling Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 52/100

nanoporetech/dorado#1623 · 8 comments · Opened Aug 12, 2026
Dorado polish does not utilize all assigned --infer-threads Open

polish

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nanoporetech/dorado#1622 · 1 comment · Opened Aug 11, 2026
dorado demux only uses single core with --no-classify when many CPUs are available Open

barcode

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nanoporetech/dorado#1620 · 4 comments · Opened Aug 8, 2026
Question regarding N1-methylpseudouridine detection support Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

nanoporetech/dorado#1618 · 1 comment · Opened Aug 3, 2026
MinKNOW 26.01.15: No basecall models are available. Possible Mooneye API problems. Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

nanoporetech/minknow_api#94 · 2 comments · Opened Aug 1, 2026
Merge demux across flowcells/according to sample sheet manifests Open

barcode

Difficulty 4/5 3-5 days Newbie friendliness 55/100

nanoporetech/dorado#1616 · 4 comments · Opened Jul 24, 2026
dorado basecaller/aligner pass through aligner/mm2 parameters in the PG tag Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

nanoporetech/dorado#1614 · 1 comment · Opened Jul 15, 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
MinKNOW 26.01.15: /var/lib/minknow/data/rpc-certs/mooneye not created during install - permission denied Open

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

nanoporetech/minknow_api#93 · 19 comments · Opened Jun 9, 2026
Low GPU usage Open

basecalling speed cluster

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

nanoporetech/dorado#1606 · 5 comments · Opened Jun 8, 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
dorado polish introduces systematic errors in dnd+ bacterial assemblies from HAC v6.0 basecalled data Open

polish

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

nanoporetech/dorado#1599 · 2 comments · 1 reaction · Opened May 28, 2026
Error: Ensure each CTC is inserted correctly before running check again Open

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

nanoporetech/minknow_api#92 · 1 comment · Opened May 26, 2026
Support pytorch-based Clair3 models Open

Difficulty 4/5 3-5 days Newbie friendliness 57/100

nanoporetech/rerio#73 · 1 comment · 2 reactions · Opened May 26, 2026
SUP v6 models? Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

nanoporetech/dorado#1595 · 12 comments · Opened May 22, 2026
Clarification on recommended modified-base model for mammalian genomic DNA Open

mods question

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nanoporetech/dorado#1592 · 4 comments · Opened May 13, 2026
Detecting Run Failures and Machine Crashes in MinKNOW Open

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

nanoporetech/minknow_api#91 · 1 comment · Opened May 7, 2026
Dorado basecaller fails on MIG GPU allocation when CUDA_VISIBLE_DEVICES contains 4 GPUs but only detects the MIG's parent GPUs Open

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

nanoporetech/dorado#1586 · 5 comments · Opened Apr 15, 2026
Possible support for alternative poly tail by extending `--estimate-poly-a` to distinguish alternative 3′ tail types and mixed tail compositions? Open

polyA

Difficulty 5/5 Over a week Newbie friendliness 30/100

nanoporetech/dorado#1583 · 1 comment · Opened Mar 27, 2026
Readuntil data reception issue Open

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

nanoporetech/minknow_api#90 · 3 comments · Opened Mar 23, 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
MinKNOW app issue - RPC handling error notification Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nanoporetech/minknow_api#89 · 1 comment · Opened Mar 20, 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
Dorado demux bams sorted differently to reference file Open

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

nanoporetech/dorado#1576 · 6 comments · Opened Mar 2, 2026
GAA repeats in Dorado output - RNASeq Open

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

nanoporetech/dorado#1575 · 14 comments · 1 reaction · Opened Feb 23, 2026
CUDA error: out of memory Open

polish

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

nanoporetech/dorado#1570 · Opened Feb 9, 2026
Unclear state of duplex demultiplexing Open

documentation

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

nanoporetech/dorado#1569 · 7 comments · Opened Feb 5, 2026
Support for over 5 channels on one computer Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

nanoporetech/minknow_api#88 · Opened Feb 4, 2026
Barcode trimming is overly aggressive Open

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

nanoporetech/dorado#1564 · 6 comments · Opened Jan 24, 2026
Output folder of demux incomprehensible Open

barcode

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

nanoporetech/dorado#1563 · 14 comments · Opened Jan 23, 2026
dorado polish - RAM of 768 GB not sufficient Open

polish

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

nanoporetech/dorado#1559 · 3 comments · Opened Jan 22, 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
Cannot perform grpc connection from WSL2 Open

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

nanoporetech/minknow_api#87 · 6 comments · Opened Dec 2, 2025
Huge difference in 6mA modification between v4.0.1_6mA@v2, v4.2.0_6mA@v3 and v5.2.0_6mA@v1 Open

mods

Difficulty 5/5 Over a week Newbie friendliness 30/100

nanoporetech/dorado#1538 · 8 comments · Opened Nov 27, 2025
File is uncompressed? Open

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

nanoporetech/pod5-file-format#184 · Opened Nov 13, 2025
No possibility to change location for tmp & intermediate files generated by MinKnow even with changed data path Open

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

nanoporetech/minknow_api#86 · 10 comments · Opened Oct 27, 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
API clients only support one server certificate at a time Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

nanoporetech/minknow_api#85 · 1 comment · Opened Oct 24, 2025
Dorado aligner gives error code -3 when merging temporary files (step needed before running dorado polish) Open

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

nanoporetech/dorado#1513 · 12 comments · Opened Oct 21, 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
dorado crashes when calling sup modifications 4mC_5mC 6mA on 5090 Open

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

nanoporetech/dorado#1507 · 13 comments · 3 reactions · Opened Sep 28, 2025

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