Galaxy |

Galaxy | Tool Preview

Repository Actions

View repository View change log Browse repository tip files Download as a .tar.gz file Download as a .tar.bz2 file Download as a zip file

Make.sra (version 1.39.5.0)

Project file:

sff - provide the original sff file:

oligos - provide an oligos file to parse your sff or fastq file by. It is required and must contain barcodes and primers:

mimarks file - you can create the template for this file using the get.mimarkspackage command:

fastq - provide the original fastq file:

bdiffs - number of differences to allow in the barcode (must be > 0; default 0):

pdiffs - number of differences to allow in the primer (must be > 0; default 0):

tdiffs - total number of differences to allow in primer and barcode (must be > 0; default 0):

ldiffs - total number of differences to allow in linker sequence (must be > 0; default 0):

sdiffs - total number of differences to allow in spacer sequence (must be > 0; default 0):

checkorient - will check for the reverse compliment of the barcode or primer in the sequence. The default is false.:

orientation - specify the sequence orientation:

platform - specify platform you are using:

This is a controlled vocabulary section in the XML file that will be generated

instrument - specify instrument:

This is a controlled vocabulary section in the XML file that will be generated

libstrategy - specify library strategy:

This is a controlled vocabulary section in the XML file that will be generated

libsource - specify library source:

This is a controlled vocabulary section in the XML file that will be generated

libselection - specify library selection:

This is a controlled vocabulary section in the XML file that will be generated

datatype - specify datatype:

This is a controlled vocabulary section in the XML file that will be generated

Trim sequences and quality scores?:

will trim to the clipQualLeft and clipQualRight values in sff file

Include scrapped sequences in your submission?:

Output logfile?:

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The make.sra creates the necessary files for a NCBI submission.