Comments (2)
Hi Amanda,
can you generate a self alignment of the canu contig selected by mitoVGP (or attach the fasta from canu). Usually this is very informative of repeats and other structures that may cause issues to mummer. We can increase the processivity of mummer with the option -z (e.g. 5000 could be a good value), if the problem is just finding the overlap within a nasty repeat.
from vgp-assembly.
I am closing since it's duplicated
from vgp-assembly.
Related Issues (20)
- time of running MITOVGP HOT 36
- how to use DNAnexus Workflow to assembly genome HOT 4
- Sex chromosome assembly HOT 3
- Chromosome status estimation HOT 8
- error in Asset HOT 3
- 10X align HOT 3
- genomescope evaluation HOT 7
- asset bionano problem HOT 2
- mitoVGP crashes on start HOT 8
- QUESTION: Does mitoVGP need pacbio RAW data (BAM) files as input? HOT 3
- plant mitochondrial genomes? HOT 6
- Runtime? HOT 1
- Clarification in documentation: Polishing phased assemblies HOT 4
- mitoVGP crashes on start HOT 4
- Possible missed documentation -- haplotype merging step HOT 4
- Pipeline for Polishing Canu assembly with Illumina Reads HOT 1
- Problem install conda environment HOT 4
- BLAST options error: File .fasta does not exist HOT 11
- telomere prediction HOT 1
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 vgp-assembly.