Hi,
I am very excited that I can share now with you my nodes and workflows that I created for NGS data analysis in KNIME.
KNIME is a workflow management system. Some of its features include:
* can handle many millions of rows on a desktop computer
* workflows can be executed from the command line
* integration with Galaxy/Mobyle possible
* workflows can be exchanged
* writing new functionality is relatively easy
* it is based on JAVA/Eclipse
* command line scripts can be organized
* no worries about naming intermediate files
* high content/ high through put problems can be already solved
* scripting in R, Perl, Python, Java, Matlab supported
* Hilighting/brushing supported
* open source
* commercial support available if desired
* support for statistics, flow control (if/while loops)
* supportive community
* creating professional looking reports
and now also:
* Reading / writing FastQ /SAM/BAM /BEDgraph files
* region of interest related tools
* AdapterRemoval
* and many more....
check it out and let me know what you think....
Installing KNIME:
Installing community nodes:
To get a quick overview of how to use it with NGS data:
NGS nodes and descriptions:
Kind regards,
Bernd
I am very excited that I can share now with you my nodes and workflows that I created for NGS data analysis in KNIME.
KNIME is a workflow management system. Some of its features include:
* can handle many millions of rows on a desktop computer
* workflows can be executed from the command line
* integration with Galaxy/Mobyle possible
* workflows can be exchanged
* writing new functionality is relatively easy
* it is based on JAVA/Eclipse
* command line scripts can be organized
* no worries about naming intermediate files
* high content/ high through put problems can be already solved
* scripting in R, Perl, Python, Java, Matlab supported
* Hilighting/brushing supported
* open source
* commercial support available if desired
* support for statistics, flow control (if/while loops)
* supportive community
* creating professional looking reports
and now also:
* Reading / writing FastQ /SAM/BAM /BEDgraph files
* region of interest related tools
* AdapterRemoval
* and many more....
check it out and let me know what you think....
Installing KNIME:
Installing community nodes:
To get a quick overview of how to use it with NGS data:
NGS nodes and descriptions:
Kind regards,
Bernd
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