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Trim.flows (version 1.39.5.0)

flow - flowgram data:

Use sffinfo to generate flow data from an sff file

Trim with an oligos file?:

a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words "forward", "reverse", and "barcode" or it can start with a "#" to tell mothur to ignore that line of the oligos file

minflows - Minimum number of flows that each sequence must contain to make it in to a "trim" file. (default 450):

(Quince uses 360)

maxflows - Maximum number of flows after which all other flows should be ignored (default 450):

(Quince uses 360 for GSFLX and 720 for Titanium)

maxhomop - Maximum homopolymers:

signal - treat any intensity signal greater than this threshold as a real signal:

Optional. Between 0 an 1. Default .5

noise - treat any intensity signal less than this threshold as noise:

Optional. Between 0 and 1. Default .7

order - flow order for nucleotides in the sequencer:

default is A, was TACG. Also accepts B or I

fasta - translate the flowgram data to fasta sequence format:

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.flows command is analogous to the trim.seqs command, except that it uses the flowgram data that comes bundled in the sff file that is generated by 454 sequencing. It's primary usage is as a preliminary step to running shhh.seqs. Chris Quince has a series of perl scripts that fulfill a similar role [1]. This command will allow you to partition your flowgram data by sample based on the barcode, trim the flows to a specified length range, and cull sequences that are too short or have too many mismatches to barcodes and primers.