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Slimm

Generic Workflow Nodes for KNIME: SeqAn version 2.3.2.201707261654 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Species Level Identification of Microbes from Metagenomes

See http://www.seqan.de/projects/slimm for more information.

Investigates which microbial species are present from a BAM/SAM alignment file .

(c) Copyright 2014-2017 by Temesgen H. Dadi.

Web Documentation for Slimm

Options

version-check
Turn this option off to disable version update notifications of the application.
mapping-files
directory containing various mapping files (names.dmp and nodes.dmp).
bin-width
Set the width of a single bin in neuclotides.
min-reads
Minimum number of matching reads to consider a reference present.
rank
The taxonomic rank of identification
cov-cutoff
the quantile of coverages to use as a cutoff smaller value means bigger threshold.
directory
Input is a directory.
output-raw
Output raw reference statstics
verbose
Enable verbose output.

Input Ports

[]

Output Ports

output path prefix. [*,Inactive]

Views

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

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: SeqAn from the following update site:

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