0 ×


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

Calculated consecutive regions of coverage from alignment file IN.bam and write regions of interst to file OUT.roi. Counting is performed over the entire region (including intron and N-regions) based on the CIGAR string of the alignment record.

Web Documentation for Bam2roi


Turn this option off to disable version update notifications of the application.
Verbose mode.
Very verbose mode.
Calculate strand-specific ROIs (see section Strand Specificness below.
Ignore paired information. Also see Section ROI Creation Details.
Link over skipped bases in the read alignment.

Input Ports

SAM/BAM formatted file. Must be sorted by coordinate. [bam,sam,sam.bgzf,sam.gz]

Output Ports

Output file with regions of interest. [roi,roi.bgzf,roi.gz]


Bam2roi Std Output
The text sent to standard out during the execution of Bam2roi.
Bam2roi Error Output
The text sent to standard error during the execution of Bam2roi. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Incoming)

  • SamToBam (50 %) 
  • SortBam (50 %) 


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


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

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.


You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.