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Make.contigs (version 1.39.5.1)

Select a way to provide forward and reverse fastq files ?:

Forward reads:

Reverse reads:

align - Select a pairwise alignment method:

Trim with an oligos file?:

match - Pairwise alignment reward for a match:

mismatch - Pairwise alignment penalty for a mismatch:

gapopen - Pairwise alignment penalty for opening a gap:

gapextend - Pairwise alignment penalty for extending a gap:

Renames sequences:

reduce file sizes and greatly reduce the size of the column formatted distance matrix downstream. Uses the rename.seqs command to rename which creates a map file so you can revert to original names at any time

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.contigs command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.

v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file.