shenwei356 / shenwei356/LexicMap
PacBio HiFi read mapping - scaling to larger dataset?
Nobody has claimed this yet.
- Dominant language
- Go
- Stars
- 227
- Forks
- 12
- Avg merge
- 1m
- Merged PRs (30d)
- 1
Description
I have a eukaryote-derived long read metagenome set I am interested in mapping against ATB to isolate bacteria-only sequences. The reads are PacBio HiFi, mean length 17.5 kb and there are 5k reads in the set. I'm using AWS to mount and query the LexicMap ATB index so I'm trying to keep costs low. After reading more of the LexicMap documentation I wonder if these reads are too long or the overall set of 5k is too large to map with LexicMap in 24/48 hrs? Would it be better to remove host reads another way (like Deacon/Hostile) and then map a smaller set with LexicMap? I appreciate any advice you might have for me. Thanks
Contributor guide
No contributing guide indexed for this repository
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.
Research direction
The issue names no source files, tests, or entry points. Start by reviewing the LexicMap documentation and the AWS-mounted ATB workflow described in the report, then determine whether 5,000 PacBio HiFi reads can be mapped within 24–48 hours. A useful outcome would be documented guidance on feasibility and whether host-read removal should precede mapping.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- aws
- Domain
- bioinformatics, cloud, search
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100