IBIS Helmholtz-Node extension for KNIME Workbench version 22.214.171.124707071203 by IBIS KNIME Team
Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are:
Trim Galore is now also available from GitHub. You are invited to leave comments, feature request or bug reports over there!
•For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too
•For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation
•For any kind of FastQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter- and quality trimming
•The Phred quality of basecalls and the stringency for adapter removal can be specified individually
•Trim Galore! can remove sequences if they become too short during the trimming process. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality
•Trim Galore! can trim paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments with Bowtie 1
•Trim Galore! accepts and produces standard or gzip compressed FastQ files
•FastQC can be run on the resulting output files once trimming has completed (optional)
To use this node in KNIME, install KNIME4NGS from the following update site:
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.
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.
Do you have feedback, questions, comments about NodePit, want to support this platform, or want your own nodes or workflows listed here as well? Do you think, the search results could be improved or something is missing? Then please get in touch! Alternatively, you can send us an email to email@example.com, follow @NodePit on Twitter, or chat on Gitter!
Please note that this is only about NodePit. We do not provide general support for KNIME — please use the KNIME forums instead.