BROCC

eagle-i ID

Resource Type

Properties

1. Resource Description

   BROCC is a flexible software pipeline for classifying single cell eukaryotes in microbiome samples that easily interfaces with the popular QIIME pipeline. BROCC classifies amplicons using BLAST searches against large and relatively uncurated databases. BROCC uses blastn, but output from other versions of BLAST such as blastx can be substituted. BROCC first filters input BLAST hits for sufficient coverage and identity to the query sequence. If a query sequence has too many hits that are below the preset coverage threshold (70% default), or BLAST did not return a hit, it is not classified, and a message is written to the output file. BROCC then determines the identity and taxonomic hierarchy of each high quality hit using a local user installed sql database and NCBI’s e-fetch tool. BROCC then votes on the quality filtered BLAST hits, starting at the species level. At each level of the taxonomy BROCC requires the taxon with the most votes to surpass a user specified threshold for that level in order to accept it as a valid classification. If a sufficient majority is not reached, BROCC will not make a classification for that level and iterate to the next higher taxonomic level for another round of voting. BROCC filters are independently configurable at the genus and species levels, and another filter can be assigned for the remaining taxonomic levels. BROCC also contains a user modifiable list of high level and partial assignments in its configuration file. These assignments are ignored at lower taxonomic levels where they are uninformative and can distort voting, but included in higher levels. For example, a sequence read with a kingdom level assignment only is excluded up to the kingdom level, at which point the vote is counted in the kingdom assignment. In cases where the proportion of high level and partial assignments exceeds a given threshold (default 0.70), the query sequence is unassigned and marked accordingly. BROCC output includes both files containing classifications with standardized taxonomy (domain, kingdom, phylum, class, order, family, genus, species) and a second with the complete NCBI taxonomy, which includes subtaxa, supertaxa, and unranked intermediate taxonomic levels. The third file contains a log of the voting record, including how many votes were cast, how many votes the winning taxon received, and how many generic classifications were ignored for each query sequence. This file also indicates those queries that were unclassified. Both taxonomy files are suitable for use in the QIIME pipeline (i. e. they are in the same format as the output classifications as the QIIME assign_taxonomy.py script). The BROCC program is implemented in Python version 2.7. It queries the NCBI taxonomy and requires local installations of SQL and BLAST.

2. Additional Name

   BLAST Read and OTU Consensus Classifier

3. Used by

   Bushman Laboratory

4. Version

   1.1.0

5. Operating System

   Unix

6. Data Input

   Amplicon-based sequence sets

7. Data Input

   BLAST results, output format 7

8. Data Output

   QIIME-formatted taxonomy map

9. Data Output

   Log file with full classification and voting details

10. Data Output

    NCBI taxonomy file

11. Software purpose

    Sequence-based phylogenetic analysis objective

12. Related Publication or Documentation

    A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples

13. Website(s)

    http://sourceforge.net/projects/brocc/

14. Related Technique

    Metagenomics analysis

15. Developed by

    Bushman, Frederic D., PhD

16. Developed by

    Bittinger, Kyle, PhD

17. Developed by

    Dollive, Serena

18. Software license

    GNU General Public License

19. Coded in

    Python