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Seqcons

Web Documentation for Seqcons

Options

method: alignment method
bandwidth: bandwidth
noalign: no align, only convert input
matchlength: min. overlap length
quality: min. overlap precent identity
overlaps: min. number of overlaps per read
window: The window size. If this parameter is greater than 0 then all overlaps within a given window are computed.
include: include contig sequence
rmethod: realign method

Input Ports

: file with reads [fa,fasta,opt.]
: message file [afg,opt.]
: Sam file [sam,opt.]
: FASTA file with contigs, ignored if not Sam input [fa,fasta,opt.]

Output Ports

: output filename [afg,seqan,cgb,sam]

Popular Predecessors

Popular Successors

Views

Seqcons Std Output: The text sent to standard out during the execution of Seqcons.
Seqcons Error Output: The text sent to standard error during the execution of Seqcons. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

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Developers

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Installation

To use this node in KNIME, install the extension SeqAn from the below update site following our NodePit Product and Node Installation Guide:

v4.7

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Plugin version: 2.4.1.202004061533

On NodePit since: 2022-12-06

Last update: 2024-04-13

KNIME versions: From v3.6 to v4.7

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