0 ×

RawReadManipulator

IBIS Helmholtz-Node extension for KNIME Workbench version 1.8.1.201707071203 by IBIS KNIME Team

This node is based on the RawReadManipulator tool (written by Jonathan Hoser). It filter reads from a fastQ or fastA file and creates a new fastQ/fastA file in the same directory, unless otherwise specified.

Options

Filter settings file
Choose whether to use filter settings calculated by FASTQC (in-port) or to specify your own filter settings file. If you decide to use your own filter settings, you have to set the path to the filter settings file.
Barcode file
Choose whether to split and trim reads by barcode. The barcodes must be specified in a BARCODE file
Barcodes should have the following format:
ID BARCODE(line End)
'#' marks a commentline

Parameters

Remove Adapters
This option enables you to remove adapters from reads (start and end only). Specify adapters in a comma-separated list (e.g "CAGGTACG,CATTTTAG,AAATTGGAC").
Trim 3'/5' Poly-A/T prefixes
This option can be covered by the filter settings.
Specify whether PolyA/T prefixes/tails at the 5' end or PolyA/T at the 3' end of the reads should be trimmed.
Discard reads with average quality below threshold
This option enables you to define a minimum average threshold in order to remove reads with low quality. Reads with an average read quality (mean over all single read-bases) below the defined threshold are discarded
Trim reads from right until quality threshold is reached
This option enables to trim reads by quality by defining a quality threshold. The reads can either be trimmed from only the right or from both sided ('Also trim from left') until a quality value above the set threshold is encountered. Also trim from left"> Reads are trimmed from both sides applying the threshold set in "Trim reads by quality"
Reads containing Ns
Determine whether to remove reads containing unknown bases (Ns).
Keep single ends if partner is discarded
In case of paired-end data sets you can define whether to keep single ends even though the partner is discarded.
Discard reads shorter than a given length
This option enables you to discard reads of a length shorter than a define minimum read length. This trimming process is performed after all other trimming operations.
Options for Illumina-data
In case of Illumina data: Specify the quality encoding, if known. If its set to 'auto', the node will make an educated guess.
Define whether the quality encoding should be converted to phred-based qualities.
Thread number
Set the number of threads be used.
Optional output folder for RRM
Choose whether the output files should be stored in a separate output folder. In this case set the path to the folder.

Preference page

HTE
Set a threshold for repeated execution.Only used if HTE is enabled in the preference page.

Input Ports

Icon
Cell 0: Path to ReadFile1
Cell 1 (Optional): Path to ReadFile2
Cell 2 (Optional): Path to FilterFile

Output Ports

Icon
Cell 0: Path to ReadFile1
Cell 1: Path to ReadFile2 (if given)

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install KNIME4NGS from the following update site:

KNIME 4.3

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.