Comments (3)
from quickmerge.
Hi,
Thanks for replying me. Yes, I found that lowering the cutoff 2M doesn't introduce more duplicated sequence. So it's fine. But I recently realised that those places that can't be merged are mostly heterozygous places. For example, the reference assembly has seq1(haplotype A) + seq2(haplotype A) in one contig, however the query assembly has contig1(haplotype A) and contig2(haplotype B). Though the reference assembly remains the alternative allele of seq2 (could be aligned to contig2(haplotype B) in query assembly) in the whole genome file as a small contig, but the contig1 and contig2 from query assembly will still not be merged together, as it lacks hints where this haplotype B should be placed.
I'm not sure how I can solve this problem without generating a phased assembly (our species is highly inbred). But I do have quite some gaps because of this reason, though the reference genome are pretty gapless but not with high QV. Do you think whether we could employ gfa file in this case?
from quickmerge.
I have not really experimented with gfa file in this context. I will have to think about it.
from quickmerge.
Related Issues (20)
- Unexpected sequence in merged fasta HOT 2
- quickmerge ( multiple long-read only ) + ( multiple hybrid ) assemblies
- ERROR: mummer and/or mgaps returned non-zero
- Does running iterations of quickmerge on quickmerge output create artifacts? HOT 3
- Quickmerge before or after haplotype purging for high heter rate plant assemblies? HOT 1
- quickmerge: terminate called after throwing an instance of 'std::out_of_range' HOT 6
- Is there any problem to use quickmerge and give in input a previous output of quickmerge?
- Problem with Reference and Query
- segment fault and Core dump HOT 3
- Confusion about argument ```-l``` and ```-ml``` HOT 3
- [Mac] Running merge_wrapper.py in conda : No such file or directory: 'nucmer': 'nucmer' HOT 3
- quickmerge aborted HOT 8
- Is there a history of merges not included in anchor_summary.txt? HOT 1
- Output problems HOT 2
- terminate called after throwing an instance of 'std::out_of_range' HOT 7
- Quickmerge fails to set its PATH internally HOT 6
- core dump at final step HOT 3
- Aborted (core dumped) quickmerge HOT 5
- Program runs, but doesn't provide correct output HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from quickmerge.