nanoporetech/dorado

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Oxford Nanopore's Basecaller

Stars: 875
Forks: 129
Open beginner issues: 0
Indexed issues: 90

Dominant language: C++
License: No license data
Last GitHub push: Aug 26, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: help wanted
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

90 open issues indexed

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
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
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
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
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
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
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
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
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
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
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
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
strand biased basecalling errors Open

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

nanoporetech/dorado#1505 · 2 comments · Opened Sep 26, 2025
Options to set scoring manually Open

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

nanoporetech/dorado#1487 · 2 comments · Opened Sep 7, 2025
Dorado correct (CPU) c10::Error Open

read_correction

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

nanoporetech/dorado#1481 · 6 comments · Opened Sep 2, 2025
Poly(A) tail estimation post basecalling Open

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

nanoporetech/dorado#1475 · 1 comment · Opened Aug 25, 2025
Barcode sequence related bias of polyA tail length estimation Open

polyA

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

nanoporetech/dorado#1473 · 14 comments · Opened Aug 22, 2025
Create `.csi` index when using dorado aligner Open

aligner

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

nanoporetech/dorado#1465 · 3 comments · 3 reactions · Opened Aug 20, 2025
dorado Distribution: Conda Package (bioconda) Open

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

nanoporetech/dorado#1464 · 10 reactions · Opened Aug 20, 2025
Missing SM-tag for single samples Open

documentation

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

nanoporetech/dorado#1462 · Opened Aug 18, 2025
time estimate calculation is wrong when resuming Open

resume

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

nanoporetech/dorado#1461 · 1 comment · Opened Aug 15, 2025
UMI detection doesn't work when performing barcode detection with `dorado demux` Open

barcode trim

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nanoporetech/dorado#1438 · 2 comments · Opened Jul 22, 2025
CUDA error: invalid argument Open

duplex

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

nanoporetech/dorado#1437 · 6 comments · Opened Jul 21, 2025
Missing or outdated BAM metadata in dorado demux output Open

barcode

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

nanoporetech/dorado#1404 · 3 comments · Opened Jun 26, 2025
Provide `--resume-from` flag for polish command Open

polish

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

nanoporetech/dorado#1391 · Opened Jun 10, 2025
Basecaller performance issues with `--resume-from` option Open

basecalling speed

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

nanoporetech/dorado#1390 · 1 comment · Opened Jun 10, 2025
CUDA illegal memory access error in Dorado 0.9.1 and 1.0.0 Open

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

nanoporetech/dorado#1386 · 5 comments · 1 reaction · Opened Jun 5, 2025
GH200 Arm64 Dorado Binary: Unsupported system page size <jemalloc> Open

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

nanoporetech/dorado#1377 · 1 comment · Opened May 29, 2025
Tandem Modifications in Dorado Predictions Open

mods

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

nanoporetech/dorado#1376 · 15 comments · Opened May 29, 2025
dorado aligner/polish: @RG header examples please Open

documentation polish

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

nanoporetech/dorado#1363 · 2 comments · Opened May 22, 2025
dorado basercaller: what(): std::bad_alloc -> Core dumped Open

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

nanoporetech/dorado#1344 · 2 comments · Opened Apr 29, 2025
Seeing modified bases in an in-vitro transcribed RNA Open

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

nanoporetech/dorado#1335 · 6 comments · Opened Apr 20, 2025
Sequence strand bias in ~600 bp repetitive regions Open

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

nanoporetech/dorado#1320 · 5 comments · 2 reactions · Opened Apr 7, 2025
m6A and Inosine Overlap in Basecalling Results Open

mods

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

nanoporetech/dorado#1310 · 5 comments · Opened Apr 2, 2025
Various errors on dorado basecaller RNA hac 5.1 for m6A with 4090 Open

data

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

nanoporetech/dorado#1296 · 4 comments · Opened Mar 24, 2025
Feature: Dual Barcoding support Open

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

nanoporetech/dorado#1272 · 2 comments · 1 reaction · Opened Mar 6, 2025

nanoporetech/dorado

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