GASiC

Read correction node for the GASiC approach. The node takes a normalized read count vector and a similarity matrix for the genomes and computes a corrected abundance vector for the given species.

Options

Cobyla Options

Rho Begin

Initial Variables Change.

Rho End

Convergence criteria.

Max. Iterations

Maximal number of iterations for the optimization.

Bootstrapping Options

Number of iterations

Number of bootstrap samples.

p-value computation

test level

Abundance from species are treated as not present. Needed for p-value computation.

Mutlithreading Options

Number of Threads

The number of threads that should be used to optimize the correction values.

Input Ports

Table containing for each read the information to which genomes it maps.

Table containing for simulated reads from which genome they were simulated and to which genomes they map.

Output Ports

Corrected abundance values.

Best Friends (Incoming)

• GASiC (43 %) 
• GASiCListReader (29 %) 
• GASiCReader (14 %) 
• Bash (14 %) 

Best Friends (Outgoing)

• GASiC (75 %) 
• Substructure Search (25 %) 

Workflows

• GASiC (SeqAn) 

Installation

To use this node in KNIME, install GASiC Nodes for KNIME 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.

Developers

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