BBMap | BBMap short read aligner , and other bioinformatic tools | Genomics library

by BioInfoTools Java Version: v35.85 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(4)Vulnerabilities Install Support

kandi X-RAY | BBMap Summary

BBMap is a Java library typically used in Artificial Intelligence, Genomics applications. BBMap has no bugs, it has no vulnerabilities and it has low support. However BBMap build file is not available and it has a Non-SPDX License. You can download it from GitHub.

The official source of BBTools is here:.

Support

Quality

Security

License

Reuse

Support

BBMap has a low active ecosystem.

It has 174 star(s) with 112 fork(s). There are 11 watchers for this library.

It had no major release in the last 12 months.

There are 28 open issues and 9 have been closed. On average issues are closed in 12 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of BBMap is v35.85

Quality

BBMap has no bugs reported.

Security

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

License

BBMap has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

BBMap releases are available to install and integrate.

BBMap has no build file. You will be need to create the build yourself to build the component from source.

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

Top functions reviewed by kandi - BETA

kandi has reviewed BBMap and discovered the below as its top functions. This is intended to give you an instant insight into BBMap implemented functionality, and help decide if they suit your requirements.

Parse the command line arguments
Get the appropriate extension code for the extension
Parse the readgroup properties
Set the system path
Calculates the affine score based on the base location and base locations
Scores the set of indices without indels
Calculates the AffineScore from the positions of the positions of the nucleotide
Mate the two reads
Methode pair
Run the analysis
Generate a score based on an alignment
Main method for testing
Extends the sequence of bases to the right - hand side
Process a single read read
Extend a sequence of bases to the right - hand side
Generate a score for a given read
Process a read of a specified read
Process a read
Generate a set of bins from the given read
Replaces all the inputs
Create a list of variables from a read
Process a read pair
Main method for testing
Prepare the arguments
Run the task
Process the specified read

Get all kandi verified functions for this library.

BBMap Key Features

No Key Features are available at this moment for BBMap.

BBMap Examples and Code Snippets

No Code Snippets are available at this moment for BBMap.

Community Discussions

Trending Discussions on BBMap

How to extract strings by using awk on multiple text files and summaries to one file

Using basename and absolute path inside a for loop at the same time

How to include shell script suite in docker file

Add file by (*) star character to variable in for loop

QUESTION

How to extract strings by using awk on multiple text files and summaries to one file

Asked 2021-Nov-02 at 13:32

I have 70 input files, file names are as like slurm-22801576.out, slurm-22801573.out, slurm-26801571.out, and so on. I want to extract all desired strings to one file. So I did the following but I was able to do so for one file only. How to do that on multiple files?

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ANSWER

Answered 2021-Nov-02 at 13:32

You may use this awk:

Source https://stackoverflow.com/questions/69809395

QUESTION

Using basename and absolute path inside a for loop at the same time

Asked 2021-Apr-02 at 22:55

Let's say I have

...

ANSWER

Answered 2021-Apr-02 at 22:55

Use parameter expansion to manipulate the names. ${i%_1.fq.gz} will remove the suffix from $i, and ${i##*/} gives you the basename. eg:

Source https://stackoverflow.com/questions/66926090

QUESTION

How to include shell script suite in docker file

Asked 2020-Nov-06 at 00:24

I am trying to create a docker image for BBMAP (https://sourceforge.net/projects/bbmap/files/latest/download) shell script suite available online along with samtools and picard.jar. I was able to run samtools and picard, but for some reason I am not able to add bbmap below. Can someone please let me know what I am missing here?

I am trying to add shell scripts to bin to run them as executables. In my docker file below, this is where I need help:

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ANSWER

Answered 2020-Nov-06 at 00:24

Earlier in your script, you run:

Source https://stackoverflow.com/questions/64706962

QUESTION

Add file by (*) star character to variable in for loop

Asked 2020-Sep-30 at 14:24

I have a folder structure where two files are in a folder. The files have long names, yet are distinguished by R1 and R2. Note I am running this over many folders using the for loop but keeping it simple for this example. I am running a loop and am wonder how to correctly call the files with a (*) star character to autocomplete without having to type in all file name. My attempt is below:

...

ANSWER

Answered 2020-Sep-30 at 05:42

If you want only two files from your folder_structure, then i believe it would be good to use find to search for the files and assign then into separate variables as per your requirement...don't see use of for loop here.

Source https://stackoverflow.com/questions/64131133

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

Vulnerabilities

No vulnerabilities reported

Install BBMap

You can download it from GitHub.
You can use BBMap like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the BBMap component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .

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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