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.

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Workflows

GASiCSeqAn

Further Links

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