centrifuge | Classifier for metagenomic sequences | Genomics library

by DaehwanKimLab C++ Version: v1.0.4 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | centrifuge Summary

centrifuge is a C++ library typically used in Artificial Intelligence, Genomics applications. centrifuge has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Classifier for metagenomic sequences. [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. The Centrifuge hompage is The Centrifuge paper is available at The Centrifuge poster is available at For more details on installing and running Centrifuge, look at MANUAL.

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Quality

Security

License

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Support

centrifuge has a low active ecosystem.

It has 207 star(s) with 72 fork(s). There are 14 watchers for this library.

It had no major release in the last 12 months.

There are 112 open issues and 133 have been closed. On average issues are closed in 63 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of centrifuge is v1.0.4

Quality

centrifuge has 0 bugs and 0 code smells.

Security

centrifuge has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

centrifuge code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

centrifuge is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

centrifuge releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

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centrifuge Key Features

No Key Features are available at this moment for centrifuge.

centrifuge Examples and Code Snippets

No Code Snippets are available at this moment for centrifuge.

Community Discussions

Trending Discussions on centrifuge

PHPIDS on php 8.1 Deprecated Errors

GAMS translated nonlinear objective function looks different than defined objective

jqGrid toobar not filtering when typing

React multiple import one module caching re-use

Django AWS Elastic Beanstalk error ImproperlyConfigured: Error loading MySQLdb module: No module named MySQLdb

QUESTION

PHPIDS on php 8.1 Deprecated Errors

Asked 2022-Feb-13 at 09:39

i got a problem with PHPIDS on a PHP 8.1 Server.

Here the Errors:

...

ANSWER

Answered 2022-Feb-13 at 09:39

As of PHP 8.1, you have to fix the return type of the functions count() and getIterator() to match with interfaces.

public count(): int (see Countable)
public getIterator(): Traversable (see IteratorAggregate)

Source https://stackoverflow.com/questions/71099351

QUESTION

GAMS translated nonlinear objective function looks different than defined objective

Asked 2021-Apr-21 at 09:36

I am studying the batchdes.lst file for MINLP model batchdes in GAMS library. The objective function is

Defining objective function obj.. cost =g= sum(j, alpha(j)*(exp(n(j) + beta(j)*v(j)))); However, in the list of equations in the .lst file is presented as ---- obj =G= objective function definition

obj.. - (25141.1498186984)*v(mixer) - (64131.2769053431)*v(reactor) - (49066.7923833869)*v(centrifuge) - (41901.9163644973)*n(mixer) - (106885.461508905)*n(reactor) - (81777.9873056449)*n(centrifuge) + cost =G= 0 ; (LHS = -230565.365179047, INFES = 230565.365179047 ****)

What kind of operation has been applied here? How the exp() translated? Is this a feature of GAMS or the Solver selected?

I implemented the same model to Pyomo and solve with the same solver from GAMS, however the Obj does not look the same in the .lst file.

Thanks!

...

ANSWER

Answered 2021-Apr-21 at 09:36

What you see here are the partial derivatives of each variable evaluated at their current level values. This comes from the GAMS documentation:

Nonlinear equations are treated differently. If the coefficient of a variable in the equation listing is enclosed in parentheses, then the corresponding constraint is nonlinear, and the value of the coefficient depends on the activity levels of one or more of the variables. The listing is not algebraic, but shows the partial derivative of each variable evaluated at their current level values.

Source https://stackoverflow.com/questions/67190755

QUESTION

jqGrid toobar not filtering when typing

Asked 2020-Oct-07 at 07:33

Using jqGrid js v5.5.0, the filter as you type functionality is not working for some fields.

Typing into the Title field causes the column to display only values that match what has been entered.

Typing a "2" into the Serial filter results in nothing being displayed.

The expected result is for the serial column to behave exactly as the title column and show partial matches.

All data is preloaded into the grid.

Here's the code and a Fiddle demonstrating the issue.

http://jsfiddle.net/rboarman/p7uyq6w2/15/

...

ANSWER

Answered 2020-Oct-07 at 07:33

The problem you have is in definition in colModel and especially the index property.

This property can't have value with space. Moreover the index property when defined is used in searching. Your definition is:

Source https://stackoverflow.com/questions/64234645

QUESTION

React multiple import one module caching re-use

Asked 2020-Aug-16 at 14:43

I am using Centrifugo websocket server. I need to connect to Centrifugo and store connection instance for future usage from from multiple components.

Will it be the good way to create this kind of export from ./socket.js?
Will centrifuge.connect() and centrifuge.setToken('') be executed if I gonna import ./socket.js module muitiple times?

./socket.js

...

ANSWER

Answered 2020-Aug-16 at 14:43

If you want to use a single instance only, it's better to import it in one place only. Best to import in the parent component and pass it as props to the children.

So your app.jsx would become:

Source https://stackoverflow.com/questions/63437837

QUESTION

Django AWS Elastic Beanstalk error ImproperlyConfigured: Error loading MySQLdb module: No module named MySQLdb

Asked 2020-May-21 at 08:01

I know this error have come to many people and I have tried different solutions and none of them worked.

I am using aws eb cli.

I am using following command eb deploy to deploy my application to server.

Following are the configuration for my Django.

under .ebextensions directory, I have following 2 files:

1: 01_packages.config

...

ANSWER

Answered 2020-Feb-24 at 19:28

Try running

Source https://stackoverflow.com/questions/60382598

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install centrifuge

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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