Freshwater microbial field guide
README
This is the README file for distribution of the arb files of the freshwater 16S rRNA gene sequence database curated by the McMahon-Bertilsson research groups. The ARB databases are useful for those who want to insert new sequences into high-quality trees with established freshwater taxonomy.
For those who want trainingset files to classify amplicons or metagenomic reads that contain 16S genes, we recommend using the Freshwater Trainingset (FreshTrain) files available in the TaxAss repo: https://github.com/McMahonLab/TaxAss. These FreshTrain files are based on the arb files contained in this repo, but have been formatted, updated, and vetted for taxonomy assignment. The TaxAss repo also includes a workflow for assigning taxonomy using the FreshTrain files. More information on the TaxAss workflow is available in our msphere paper.
The following files have been posted to this Gihub repository:
(updates added so that the most recent one is at the top)
(updated February 2016)
See here for new and better workflow: https://github.com/McMahonLab/TaxAss
FWonly_11Feb2016_1452_ready.fasta Only FW sequences. Contains 1452 sequences. Added and curated ~300 sequences from Ryan Newton.
FWonly_11Feb2016_1452.taxonomy Only FW sequences. Contains 1452 sequence IDs. Some typos and inconsistencies have been fixed.
(updated 19 July 2012)
FW_trainingset_MMBR_strict_12July12.fasta Only FW sequences, derived from 28Dec11 version. Contains 1148 sequences. Added a few new reference sequences. Fixed a few errors that made it difficult to blend FW with GG.
FW_trainingset_MMBR_strict_12July12.taxonomy Taxonomy file that goes with FW_trainingset_MMBR_strict_12July12.fasta. Note that I had to modify slightly to make it compatible with QIIME (removing extra spaces).
(updated 20 January 2012)
SSU_rRNA_FWonly_27Dec11_todistribute.arb - 11587 sequences Only FW sequences. The corresponding trainingst below was created with the ARB configuration called FW_only_25Dec2011. This excludes the "Minor Phyla", Cyanobacteria, and "AllOtherPhyla" trees because they are not FW-specific enough to justify having them in this special trainingset. Also remove "Soil_I" and "Common Isolates" within the actinos. Total: 1117 sequences.
FW_trainingset_MMBR_strict_28Dec11.fasta Only FW sequences, derived from the 9Sept11 version but with only 1117 sequences (see description of the FW_only_25Dec2011 configuration, above). Taxonomies curated to include markups like k__, p__, c__ to match greengenes. This was done to allow merging at coarser levels of resolution.
FW_trainingset_MMBR_strict_28Dec11.taxonomy Taxonomy file that goes with FW_trainingset_MMBR_strict_28Dec11.fasta. Note that I had to modify slightly to make it compatible with QIIME (removing extra spaces).
I am not uploading a concatenated FW-GG trainingset right now because my group has started doing the assignments serially. That is, we use the FW-only trainingset first, and then anything that does not get assigned with sufficient confidence gets run through the GG trainingset. We are doing this in QIIME currently, so I am not sure how to do it in mothur. It would probably require some perl scripting. I will work on this in the next few months. In the meantime, let me know if you want a merged FW-GG trainingset and I can easily upload one.
To make things even more complicated, greengenes just released a new trainingset. Byron Crump says there are some bugs (sequences not in the taxonomy and taxonomies not represented in the sequences), so we haven't used it yet. I also prefer to work with the 97%-otu version, which doesn't seem to be availble yet for the new release. I recommend that you watch the GG website closely for updates. I'll try to also!
(updated 28 September 2011)
SSU_rRNA_FWonly_9Sept11_todistribute.arb - 11587 sequences Only FW sequences. Created by marking the "All FW in trees" configuration in SSU_rRNA_FW_3Aug11_todistribute.arb, and deleting all other sequences. The "FW4mothur2" configuration is used to export sequences and taxonomies for the trainingset. Updated the "FW4mothur2" configuration to remove one short sequence that had slipped through. Now it selects 1204 sequences.
FW_trainingset_MMBR_strict_9Sept11.fasta - 1204 sequences Only FW sequences. Created by marking the "FW4mothur2" configuration in SSU_rRNA_FWonly 9Sept11_todistribute.arb. Taxonomies curated to strictly match MMBR hierarchies. Not aligned.
FW_trainingset_MMBR_strict_9Sept11.taxonomy Taxonomy file that goes with FW_trainingset_MMBR_strict_9Sept11.fasta
FWGG_trainingset_MMBR_strict_9Sept11.fasta - 36583 sequences Combined set of FW sequences (FW_trainingset_MMBR_strict_9Sept11.fasta) plus the 97%-OTU Greengenes database (gg_97_otus_4feb2011.fasta) as suggested in Werner et al (2011) ISMEJ, with overlapping sequences deleted. Taxonomies for the FW sequences were curated to strictly match MMBR hierarchies.
FWGG_trainingset_MMBR_strict_9Sept11.taxonomy Taxonomy file that goes with FWGG_trainingset_MMBR_strict_9Sept11.fasta
(updated 3 Aug 2011)
SSU_rRNA_FW_3Aug11_todistribute.arb - 28546 sequences Based on RDP Release 8.0 SSU Prokaryotic data, with FW sequences added
SSU_rRNA_FWonly_3Aug11_todistribute.arb - 11587 sequences Only FW sequences. Created by marking the "All FW in trees" configuration in SSU_rRNA_FW_3Aug11_todistribute.arb, and deleting all other sequences. The "FW4mothur2" configuration is used to export sequences and taxonomies for the trainingset.
FW_trainingset_MMBR_strict_3Aug11.fasta - 1205 sequences Only FW sequences. Created by marking the "FW4mothur2" configuration in SSU_rRNA_FW_July11_todistribute.arb. Taxonomies curated to strictly match MMBR hierarchies. Not aligned.
FW_trainingset_MMBR_strict_3Aug11.taxonomy Taxonomy file that goes with FW_trainingset_MMBR_strict_3Aug11.fasta
FWGG_trainingset_MMBR_strict_3Aug11.fasta - 36634 sequences Combined set of FW sequences (FW_trainingset_MMBR_strict_3Aug11.fasta) plus the 97%-OTU Greengenes database (gg_97_otus_4feb2011.fasta) as suggested in Werner et al (2011) ISMEJ. Taxonomies for the FW sequences were curated to strictly match MMBR hierarchies.
FWGG_trainingset_MMBR_strict_3Aug11.taxonomy Taxonomy file that goes with FWGG_trainingset_MMBR_strict_3Aug11.fasta
-- Original posting:
SSU_rRNA_FW_July11_todistribute.arb - 28546 sequences Based on RDP Release 8.0 SSU Prokaryotic data, with FW sequences added
SSU_rRNA_FWonly_July11_todistribute.arb - 11587 sequences Only FW sequences. Created by marking the "All FW in trees" configuration in SSU_rRNA_FW_July11_todistribute.arb, and deleting all other sequences. The "FW4mothur2" configuration is used to export sequences and taxonomies for the trainingset.
FW_trainingset_July11.fasta - 1205 sequences Only FW sequences. Created by marking the "FW4mothur2" configuration in SSU_rRNA_FW_July11_todistribute.arb. Not aligned.
FW_trainingset_July11.taxonomy Taxonomy file that goes with FW_trainingset_July11.fasta
FWGG_trainingset_July11.fasta - 36634 sequences Combined set of FW sequences (FW_trainingset_July11.fasta) plus the 97%-OTU Greengenes database (gg_97_otus_4feb2011.fasta) as suggested in Werner et al (2011) ISMEJ.
FWGG_trainingset_July11.taxonomy Taxonomy file that goes with FWGG_trainingset_July11.fasta
If you find any inconsistencies or mistakes, please email Trina (contact info below).
Credits: The vast majority of work in preparing this database was done by Dr. Ryan Newton, while a PhD student in the McMahon laboratory at UW-Madison. Drs. Stefan Bertilsson and Alex Eiler contributed a large number of previously unpublished sequences to the database.
###########################################################################
If you use this database, please cite this paper:
If you are assigning taxonomy with this database, please use the versions available at https://github.com/McMahonLab/TaxAss/tree/master/FreshTrain-files and also cite this paper:
###########################################################################
Updated by Katherine (Trina) McMahon - 14 September 2014 University of Wisconsin - Madison Departments of Civil and Environmental Engineering and Bacteriology tmcmahon@engr.wisc.edu