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

This program determines for each read in the reference file if it has an entry in the provided sam files stating that it mapped. Afterwards a file is generated containing a row for each read which contains the read ID and the index of the mapped references.

Web Documentation for Sam2matrix


Turn this option off to disable version update notifications of the application.
Name of the file used as reference of the corresponding sam file. If not specified the names of the mapping files are taken

Input Ports

File containing the mappings. [sam]
File containing the reads contained in the mapping file(s). [fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam]

Output Ports

Output file. [tsv]


Sam2matrix Std Output
The text sent to standard out during the execution of Sam2matrix.
Sam2matrix Error Output
The text sent to standard error during the execution of Sam2matrix. (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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