rrwick/Badread

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a long read simulator that can imitate many types of read problems

Stars: 302
Forks: 25
Open beginner issues: 0
Indexed issues: 11

Dominant language: Python
License: GPL-3.0
Last GitHub push: Jul 24, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

11 open issues indexed

Coordinate system BadRead Open

bug

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

rrwick/Badread#40 · 1 comment · Opened Apr 24, 2026
How to handle PacBio simulated reads before mapping Open

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

rrwick/Badread#31 · 2 comments · Opened Apr 3, 2024
Documentation on post processing of simulated sequences Open

enhancement

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

rrwick/Badread#22 · 1 comment · Opened Apr 19, 2023
High Memory consumption causes computer to freeze Open

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

rrwick/Badread#21 · Opened Feb 15, 2023
Question about --glitches Open

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

rrwick/Badread#16 · Opened Jun 17, 2021
ModuleNotFoundError: No module named 'edlib' Open

bug

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

rrwick/Badread#15 · 1 comment · 4 reactions · Opened Jan 6, 2021
Organelle genome simulation Open

enhancement

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

rrwick/Badread#14 · Opened Oct 6, 2020
Can we give error percentage while simualting Oxford nanopore long reads Open

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

rrwick/Badread#12 · Opened Jul 22, 2020
What if we could generate two datasets with same reads, one with good quality and one with bad quality? Open

enhancement

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

rrwick/Badread#11 · Opened May 8, 2020
Can chimeras be formed without adapter sequences? Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

rrwick/Badread#8 · 1 reaction · Opened Dec 26, 2019
Multi-threading Open

enhancement

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

rrwick/Badread#7 · 4 comments · Opened Sep 26, 2019

rrwick/Badread

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