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Generic Workflow Nodes for KNIME: SeqAn version by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

This tool reads a set of input files in SAM or BAM format and outputs the concatenation of them. If the output file name is omitted the result is written to stdout.

(c) Copyright in 2014 by David Weese.

Web Documentation for Samcat


Turn this option off to disable version update notifications of the application.
Use BAM format for standard output. Default: SAM.
Print some stats.

Input Ports

Input SAM or BAM file (or - for stdin). [bam,sam,sam.bgzf,sam.gz]

Output Ports

Output file name. [bam,sam,sam.bgzf,sam.gz]


Samcat Std Output
The text sent to standard out during the execution of Samcat.
Samcat Error Output
The text sent to standard error during the execution of Samcat. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install SeqAn from the following update site:


A zipped version of the software site can be downloaded here.

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