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Trim.seqs (version 1.39.5.0)

fasta - Sequences:

name - Sequence representative name list:

minlength - Minimum Sequence Length (default 0, ignored if < 1 ):

maxlength - Maximum Sequence Length (default 0, ignored if < 1):

maxambig - Maximum ambiguous bases (default -1, ignored if < 0):

maxhomop - Maximum homopolymers (default 0, ignored if < 1):

keepfirst - ignored if < 0):

trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements

removelast - ignored if < 0):

removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements

Trim with an oligos file?:

Trim based on a quality file?:

flip - reverse complement the trimmed sequences:

count - a count_table:

The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. If you run trim.seqs with an oligos file that contains group labels, trim.seqs will create a new *.trim.count_table with the group information included.

logtransform:

allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform.

checkorient - search the reverse complement?:

If you are running the trim.seqs command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment.

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 trim.seqs command provides the preprocessing features needed to screen and sort pyrosequences. The command will enable you to trim off primer sequences and barcodes, use the barcode information to generate a group file and split a fasta file into sub-files, screen sequences based on the qual file that comes from 454 sequencers, cull sequences based on sequence length and the presence of ambiguous bases and get the reverse complement of your sequences. While this analysis is clearly geared towards pyrosequencing collections, it can also be used with traditional Sanger sequences.