MicroRazers

Generic Workflow Nodes for KNIME: SeqAn version 2.3.2.201707261654 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Options

version-check

Turn this option off to disable version update notifications of the application.

recognition-rate

set the percent recognition rate

seed-length

seed length

seed-error

allow for one error in the seed

forward

map reads only to forward strands.

reverse

map reads only to reverse strands.

match-N

'N' matches with all other characters

max-hits

output only NUM of the best hits

purge-ambiguous

purge reads with more than max-hits best matches

low-memory

decrease memory usage at the expense of runtime

verbose

verbose mode

vverbose

very verbose mode

alignment

dump the alignment for each match

genome-naming

Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1.

read-naming

Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1.

sort-order

Select how matches are sorted. 0 = read number, 1 = genome position.

position-format

Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space.

Input Ports

A reference genome file. [fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam]

Either one (single-end) or two (paired-end) read files. [fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam]

Output Ports

Change output filename. (use - to dump to stdout in razers format) Default: <READS FILE>.razers. [razers,sam,Inactive]

Views

MicroRazers Std Output

The text sent to standard out during the execution of MicroRazers.

MicroRazers Error Output

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

Installation

To use this node in KNIME, install Generic Workflow Nodes for KNIME: SeqAn from the following update site: