SamTools

The SamTools node enables the access to several SAMtools utilities.
For more information, see the SAMtools help page

Options

HTE: Set a threshold for repeated execution.Only used if HTE is enabled in the preference page.
Path to samtools: Set the path to the SAMtools executable (only if no inport is available)
Path to reference sequence: Set the path to the reference sequence (only if no inport is available)

STDOUT / STDERR: The node offers a direct view of its standard out and the standard error of the tool.

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.

To use this node in KNIME, install the extension KNIME4NGS from the below update site following our NodePit Product and Node Installation Guide:

v5.9

Plugin provider: IBIS KNIME Team

Plugin version: 1.8.1.201707071203

On NodePit since: 2025-12-11

Last update: 2026-01-19

KNIME versions: Since v3.6

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.