Can chimeras be formed without adapter sequences?
Nobody has claimed this yet.
Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 30/100
- Issue type
- Documentation
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- python
- Domain
- documentation
Research direction
Start with the Chimera section of the Badread documentation and review how start/end adapters are described. Verify whether the question can be answered from the project documentation or cited sources, then clarify the adapter behavior and update that section if needed.
Written by the indexing model from the issue text.
Description
Hi,
I have a general question about Nanopore sequencing, based on the documentation of Badread. I hope this is the most appropriate way to ask this!
In the Chimera section of the documentation of Badread, the following is mentioned:
"If you are using start/end adapters, they will sometimes (but not always) be added between the fragments."
Would you have any citations for this or could you explain why this would be the case in real data?
My best guess is that to be sequenced a read MUST have an adapter. In a chimera though, only the first DNA fragment of the chimera must have an adapter and therefore if a DNA fragment that escaped the adapter adding stage is joined to the first fragment this would produce a 'scar-less' chimera. Is this correct?
Thanks for your help,
Jonathan
- Dominant language
- Python
- Stars
- 302
- Forks
- 25
- PR merge metrics
- No merged PRs in 30d
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
More from rrwick/Badread
-
bug
Difficulty 3/5 1-2 days Newbie friendliness 45/100
-
Difficulty 4/5 3-5 days Newbie friendliness 20/100
-
enhancement
Difficulty 3/5 1-2 days Newbie friendliness 35/100
-
Difficulty 5/5 Over a week Newbie friendliness 25/100
-
Difficulty 4/5 3-5 days Newbie friendliness 30/100
Similar issues
-
area/auth bug comp/agent P3 platform/discord type/security
Difficulty 2/5 1-3 hours Newbie friendliness 88/100
NousResearch/hermes-agent#117848 ·
-
Difficulty 2/5 1-3 hours Newbie friendliness 74/100
bancolombia/sentinel#23 ·
-
test md OpenCI
Difficulty 2/5 1-3 hours Newbie friendliness 74/100
-
integration:quickjs org:external priority:backlog topic:code-interpreter topic:middleware type:feature
Difficulty 2/5 1-3 hours Newbie friendliness 74/100
langchain-ai/deepagents#6450 ·
-
bug client
Difficulty 2/5 1-3 hours Newbie friendliness 88/100