CONNET | Accurate Genome Consensus in Assembling Nanopore | Genomics library
kandi X-RAY | CONNET Summary
kandi X-RAY | CONNET Summary
Single-molecule sequencing technologies produce much longer reads compared to next-generation sequencing, greatly improving the contiguity of de novo assembly of genomes. However, the relatively high error rates in long reads make it challenging to obtain high-quality assemblies, and a computationally-intensive consensus step is needed to resolve the discrepancies in the reads. Efficient consensus tools have emerged in the recent past, based on partial-order alignment. In this study, we discovered that the spatial relationship of alignment pileup is crucial to high-quality consensus and developed a deep learning-based consensus tool, CONNET, which outperforms the fastest tools, based on partial-order alignment, in terms of both accuracy and speed. We tested CONNET using a 90x dataset of E. coli and a 37x human dataset. In addition to achieving high-quality consensus results, CONNET is capable of delivering phased diploid genome consensus. Diploid consensus on the above human assembly further reduced 12% of the consensus errors made in the haploid results.
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Top functions reviewed by kandi - BETA
- Main function .
- Convert to int
- Run a shell command .
- Load one phase1 file .
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Community Discussions
Trending Discussions on CONNET
QUESTION
Can I convert my Azure Synapse Dataframe into JSON ? Because when I tried it, it got an error. I'm using a script as Pandas DataFrame function df.to_json(), because I assume that Azure Synapse Dataframe same as Pandas DataFrame.
So here are the script for my synapse:
...ANSWER
Answered 2021-May-31 at 09:50A pyspark dataframe is not the same thing as a pandas dataframe.
In pyspark you should be able to do:
QUESTION
I have a dataframe with with two dimensions, A and B; however this data frame is unbalanced in that some of the values are missing because the database does not include values for all possible combinations of A and B. What I want to do is make sure the dataframe is balanced, and those elements that are missing to be filled with zeros.
I am grabbing the data for the dataframe from an sqlite database that I'm conneting to via SQLAlchemy, using the following code
...ANSWER
Answered 2021-Apr-08 at 06:20QUESTION
I am RDP'd into a workgroup computer and am trying to establish a PowerShell remoting session to a remote server, on a domain.
When I try to connect to the remote server, using one of its local admin accounts, I get the following error:
new-pssession : [IP] Connecting to remote server IP failed with the following error message : Access is denied. For more information, see the about_Remote_Troubleshooting Help topic.
When I run connect using a domain admin account, the connetion works fine.
...ANSWER
Answered 2021-Mar-29 at 21:17Drat, it was the LocalAccountTokenFilterPolicy registry entry (https://docs.microsoft.com/en-us/windows-server/manage/windows-admin-center/support/troubleshooting#using-windows-admin-center-in-a-workgroup). I had checked it on the workgroup server, not on the domain server.
QUESTION
I would like to change the hikari db pool to tomcat pool. In my property file i have a hikari.schema value defined. How do i define this config value for tomcat connetion pool? It all worked before.
The property was defined like this:
...ANSWER
Answered 2021-Mar-24 at 19:51Unlike HikariCP and DBCP2, Tomcat JDBC does not have a "default schema" property (cf. available properties).
Fortunately, since you are using PostgreSQL, you can set the default schema as connection property by:
- either adding it to the URL:
jdbc:postgresql://host:port/database?currentSchema=my-schema - or by adding
currentSchema=my-schemain theconnectionPropertiesproperty of the datasource, which in Spring YAML should look like:
QUESTION
we have an OBIEE 12.2.1.3.0 server in Linux that currently only has this OBI bundle patch applied:
29112070;OBI BUNDLE PATCH 12.2.1.3.190416
Since then, there have been 6 more bundle patches that have been released. I was wondering if each one has to be installed in the order they were released as they are considered cumulative, however on Oracles support site they show that they are all superseded by the latest, because well, they are all older than the latest bundle patch.
The latest patch is #32294042, and I was wondering if just that could be installed as it has these patches listed in the 'Bugs Fixed By This Patch" section:
...ANSWER
Answered 2021-Feb-17 at 21:26Bundle Patches are always cumulative. You can install the last one.
Generally you should try to stay up-to-date. it's not just application bugs which are fixed but also security bugs. The closer you stay to the current patch level the more secure you are.
QUESTION
I tried updating Docker for Windows to 3.1.0 (skipping 3.0.0) this week, but with this update, our development setup stopped working.
Some key points describing our setup
- Docker is running on WSL2.
- We have a docker-compose.yml for setting up the infrastructure.
- This includes Oracle database 19.3 and JBoss EAP 7.3 (JDK 11).
- The JBoss service has the ports 8080 (webserver), 8787 (Java remote debugging) and 9990 (JBoss management API) exposed and mapped in docker-compose.yml.
- We use IntelliJ for development and have the "JBoss run configuration" configured the use the above mentioned ports. IntelliJ will compile and deploy the application on demand through the JBoss management API on port 9990.
Problem
The mentioned "JBoss run configuration" is the part of this setup which stopped working under Docker for Windows 3.0.0+. It seems like IntelliJ can't connet to these ports anymore, resulting in connection timeout errors on "localhost:9990". In version 2.5.x and earlier we had no problems, I tested with both 3.0.0 and 3.1.0 without success. To verify, I uninstalled Docker and installed version 2.5.x again and it started worked again. So something must have changed in Docker for Windows for the this happen.
Edit: I should mention the problem seems to be primarily the JBoss service. The oracle database and its port mapping works and can be connected to from any database client. The container logs from the JBoss service also don't report anything problematic and the service seems to start without problem.
Questions
- Has someone some hints where to search or how to debug this problem?
- Has something experienced something similar?
- Does someone know what breaking changes were introduced starting Docker for Windows 3.0.0+?
ANSWER
Answered 2021-Feb-01 at 13:20After some try and error on multiple fronts I finally found the problem. Networking and port mapping was working as expected. The problem was the connection timeout of the JBoss CLI, which IntelliJ delegates to, that has a default timeout value of 5 seconds.
Why this timeout is a problem after upgrading to Docker Desktop 3+ I don't know. But to me it seems like in the new version of Docker there is such a massive performance degradation somewhere, that the timeout of 5 seconds was exceeded every single time, so that the error always appeared.
So my solution currently, even though it smells like a workaround, is to simply set a higher value for the timeout in IntelliJ.
How can this timeout be increased?
- in IntelliJ open the menu
Help > Edit Custom Properties..., which opens theidea.propertiesfile, where you can specify IntelliJ launch options - add the property
idea.wildfly.client.timeout=30000to this file - restart IntelliJ
QUESTION
I try to connect to a socket.io-client using the following code:
client:
...ANSWER
Answered 2021-Jan-17 at 13:55Since Socket.IO v3, you need to explicitly enable Cross-Origin Resource Sharing (CORS). https://socket.io/docs/v3/handling-cors/
QUESTION
I've almost done my first big project in React+Typescript+Redux and started it on Firebase with users and some database conneted with logged users.
It was supposed to be my project to portfolio before looking for my first dev job, but it start to be very complex. Now I have idea to use it in the future to make commercial app. So the problem is I don't want to publish my code on github, but at the same time I want to publish all my commits and repository description on Github for recrutiers (and all my tasks from trello table). Is it possible to publish only commits and description from github repository?
...ANSWER
Answered 2021-Jan-11 at 01:24No, this is not possible. If your repository is public, anyone can clone the entire repository. The only way to make your code inaccessible is to make the repository private, which means nobody can see it without having permssion.
QUESTION
I got some strange situation. When i start my spring boot app with application file:
...ANSWER
Answered 2021-Jan-03 at 13:18I got environtment variable which overrided username value
QUESTION
I am trying to deploy my app to Heroku. I am getting 503 (Service Unavailable) error even though it runs on localhost. I have tried many solutions, but none of them are working. My app.js file
...ANSWER
Answered 2020-Dec-13 at 13:14Try setting up the DB_URL in your Heroku application. Use the following command:
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Install CONNET
You can use CONNET like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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