This page contains links to the databases and supplementary files of CREST (Classification Resources for Environmental Sequence Tags). Files for each database (SilvaMod and Greengenes) are distributed as gzipped tar-files. Each default database file contains the mapping and tree-files needed for classification with the LCAClassifier or MEGAN, as well as:

• since v4, a FASTA file with all reference sequencesbinary search indececes for the, or
• CREST3 or below, binary indices formatted for the NCBI Blast+ suite

To unpack the files, use e.g.:

tar xvzf silvamod.tar.gz

For more information about CREST, please see the GitHub repository.

Default database files

• SilvaMod PR2 v138 (based on SILVA nr SSU Ref v138 and PR2 v4_13)
• BOLD (for COI, updated May 2018)
• UNITE (for fungal ITS, v7.2 2017-10-10)
• amoA

FASTA-formatted sequence files and previous version of reference databases

• SilvaMod v128 (based on SILVA nr SSU Ref v128)
• SilvaMod v128 (FASTA) (based on SILVA nr SSU Ref v128)
• SilvaMod v106
• Greengenes (v 13-8-2013)
• UNITE (v7.2 2017-10-10)
• amoA

Other supplementary files

• Metadata for microgAMBI biotic index classification
• SilvaMod v128 in ARB format
• Environmnetal datasets used for testing in Lanzen et al. 2013:
1. SSU rRNA pyrosequencing reads from the metagenome of Lake Lanier (Oh et al. 2011)
2. SSU rRNA pyrosequencing reads from the metatranscriptome of a forest soil
3. Illumina amplicon reads (16S) from Siberian tundra soil
4. Pyrosequenced amplicon reads (16S) from a deep-sea hydrothermally associated microbial mat (Lanzén et al. 2011)

For even older versions of SilvaMod (SSUrdb and LSUrdb) , please see Community profiling

• CREST Tutorial
• Instructions
• Tutorial_Dataset
• BlastResults

To cite CREST

Lanzén, A., Jørgensen, S.L., Huson, D.H., Gorfer, M., Grindhaug, S.H., Jonassen, I., Øvreås, L. & Urich, T. CREST - Classification Resources for Environmental Sequence Tags PLoS ONE, Public Library of Science, 2012, Vol. 7(11), pp. e49334

References

Lanzen, A.; Jorgensen, S. L.; Bengtsson, M. M.; Jonassen, I.; Ovreas, L. & Urich, T. (2011), 'Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA.', FEMS Microbiol Ecol 77, 577-589.