0 ×

SlimmBuild

Generic Workflow Nodes for KNIME: SeqAn version 2.4.1.202004061533 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

SLIMM Species Level Identification of Microbes from Metagenomes

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

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

Web Documentation for SlimmBuild

Options

version-check
Turn this option off to disable version update notifications of the application.
batch
maximum number of mapping to load to memory. (default=1000000)
verbose
Enable verbose output.

Input Ports

Icon
NCBI's names.dmp file which contains the mapping of taxaid to name []
Icon
NCBI's nodes.dmp file which contains the taxonomic tree. []
Icon
A multi-fasta file used as a reference for mapping [fq,fq.bgzf,fq.gz,fq.bz2,fastq,fastq.bgzf,fastq.gz,fastq.bz2,fa,fa.bgzf,fa.gz,fa.bz2,fasta,fasta.bgzf,fasta.gz,fasta.bz2,faa,faa.bgzf,faa.gz,faa.bz2,ffn,ffn.bgzf,ffn.gz,ffn.bz2,fna,fna.bgzf,fna.gz,fna.bz2,frn,frn.bgzf,frn.gz,frn.bz2,embl,embl.bgzf,embl.gz,embl.bz2,gbk,gbk.bgzf,gbk.gz,gbk.bz2,raw,raw.bgzf,raw.gz,raw.bz2,sam,sam.bgzf,sam.gz,sam.bz2,bam]
Icon
one ore more accession to taxa id mapping files dowloaded from ncbi (separated by space.) []

Output Ports

Icon
The path to the output file (default slimm_db.sldb) [sldb]

Views

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

Installation

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

KNIME 4.3

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.

Developers

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.