0 ×

Bio Sequence Reader

NGS related nodes for KNIME Workbench version 0.2.200.qualifier by Bernd Jagla, Institute Pasteur

Reads a sequence file into two columns: seq_name and sequence

This implementation uses the Biojava (VERSION 1.7.1) implementation for reading the data

It creates a sequence object that can be accessed by special nodes

The following file formats can be read in Fasta Genbank uniprot embl INSDseq

you also have to specify if the sequences are RNA, DNA, protein sequences

Annotations are stored with the sequence objects

Sample code to access annotation

Sample code to access sequence information

Large sequence files with lots of annotations might not fit into memory


File name
Filename of sequence file
Sequence type (RNA, DNA, Protein)
File format (FASTA, Genbank, Uniprot, embl, INSDseq)
Limit the number of entries to read in. (0=all)

Output Ports

Sequence object representation of the input file

Best Friends (Incoming)

Best Friends (Outgoing)


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


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.


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.