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README.md
mothur2oligo.sh
renamer.pl

README.md

This is a shell script for transforming mothur output to appropriate format for A. murat Eren's oligotyping pipeline. To successfully run this script, follow the instructions below.

Files:

You will need access to the following mothur files to run this script. The examples of file names pertain to the Mothur Miseq SOP:
- taxonomy file: stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy
- count file: stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.count_table
- fasta file: stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta

Important: Mothur uses a "preclustering" step before taxonomy assignment to reduce the number of uique sequences and therefore computational time and memory. Essentially it merges rare sequences that differ by one or two nucleotides. These rare sequences are likely to be sequencing errors rather than true sequence variants. However, oligotyping is designed to handle these rare variants through its own algorithm and filtering mechanism. Depending on your data and research question, you may want to rerun mothur, skipping the preclustering step, to be sure you are discovering all of the oligotypes of interest. Based on very limited personal experience, the sequences that are joined during preclustering are usually ones you would filter out with the -M parameter in the oligotyping software. You should not take this for granted with your own data though.

Steps:

  1. Copy all the mothur files listed above into the same directory as this one
  2. Edit mothur2oligo.sh and fill in the appropriate file names and taxon info at the top.
  3. Once you have run this full script, you can use the '*_headers-replaced.fasta' file in the oligotyping pipeline

Note: Mothur must be in your path

Instructions for downloading the oligotyping software are here

Instruction for running the oligotyping software are here

Any questions? contact michberr8@gmail.com

Credits:

perl script from http://www.perlmonks.org/?node_id=975419
Sharon Grim helped with this shell script
Oligotyping pipeline: http://merenlab.org/projects/oligotyping/