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Protocols

BROCC specifications

Information


Unique identifier OMICS_14733
Name BROCC
Alternative name BLAST Read and Operational Taxonomic Unit Consensus Classifier
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data BLAST results
Output data Outputs a QIIME-formated taxonomy map and a log file
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Frederic Bushman

Publication for BLAST Read and Operational Taxonomic Unit Consensus Classifier

BROCC citations

 (6)
library_books

Warming, shading and a moth outbreak reduce tundra carbon sink strength dramatically by changing plant cover and soil microbial activity

2017
Sci Rep
PMCID: 5700064
PMID: 29167456
DOI: 10.1038/s41598-017-16007-y

[…] taxonomic resolution. Alignment parameters were modified from default: Word size = 11, reward = 2, gapopen = 4, gapexted = 2. Hits with e-value < 10−5 were discarded. Taxonomy was voted upon with the BROCC 1.1.0 pipeline with the default ‘amplicon’-mode parameters. This resulted in re-classification of 113 OTUs, accounting for 11% of the dataset. Another 113 OTUs (0.25%) were classified outside th […]

call_split

Improved characterization of medically relevant fungi in the human respiratory tract using next generation sequencing

2014
Genome Biol
PMCID: 4232682
PMID: 25344286
DOI: 10.1186/s13059-014-0487-y
call_split See protocol

[…] atch the sample-specific barcode sequence and the leading ITS primer sequence exactly. The reads were clustered by similarity at the 97% level using UCLUST []. Taxonomic assignments were generated by BROCC [], after BLASTing representative ITS sequences to the nt database from NCBI (maximum e-value of 10−5, maximum 100 results per query).For the 16S amplicon, reads were similarly filtered, but a m […]

call_split

Fungi of the Murine Gut: Episodic Variation and Proliferation during Antibiotic Treatment

2013
PLoS One
PMCID: 3747063
PMID: 23977147
DOI: 10.1371/journal.pone.0071806
call_split See protocol

[…] with the QIIME software package using default parameters except where indicated, and using R. Fungal reads were queried against the nt database using NCBI’s blastn tool and then classified with the BROCC classifier .Eukaryotic PCoA analysis was performed using taxonomic relationship corresponding to the NCBI Taxonomy . Because de novo tree construction using the ITS1 region is not feasible due t […]

library_books

The human mycobiome in health and disease

2013
Genome Med
PMCID: 3978422
PMID: 23899327
DOI: 10.1186/gm467

[…] nalyses; and determination of fungal diversity within and across groups (referred to as α and β diversities) [,]. In addition, pipelines that are specific for mycobiome studies, such as CloVR-ITS and BROCC, have been developed recently [,]. A database against which the amplified sequences can be compared must also be selected, but a database as rich as that for bacterial 16S rDNA is still lacking […]

call_split

Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents

2013
PLoS One
PMCID: 3684604
PMID: 23799070
DOI: 10.1371/journal.pone.0066019
call_split See protocol

[…] idered for further analysis if they had a minimum of 5 sequences detected across all samples. Taxonomy was assigned to OTU representative sequences using the RDPclassifier for archaeal sequences and BROCC for fungal sequences. All taxonomy assignments were manually curated to check for accuracy and nomenclature using BLASTn against GenBank’s NR/NT database. For Archaea, the taxonomic assignment […]

library_books

Succession in the Gut Microbiome following Antibiotic and Antibody Therapies for Clostridium difficile

2012
PLoS One
PMCID: 3468616
PMID: 23071679
DOI: 10.1371/journal.pone.0046966

[…] was amplified with the 18S_0067a_deg/NSR399 primer pair and initially worked up through the QIIME metagenomic analysis pipeline . Taxonomic assignments were made using top BLAST hits as well as with BROCC, a pipeline for taxonomic assignment using voting on percent identity of the best BLAST hits . The populations of single cell eukaryotes have not been studied extensively for hamster gut; theref […]

Citations

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BROCC institution(s)
Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Division of Gastroenterology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
BROCC funding source(s)
This work was supported by Project UH2DK083981, the Penn Genome Frontiers Institute; NIH AI087990, AI083480, U01AI095608; NIH AI39368; T32-AI060516; Penn Digestive Disease Center (P30 DK050306); The Joint Penn-CHOP Center for Digestive, Liver, and Pancreatic Medicine; S10RR024525; UL1RR024134, K24-DK078228; and the Howard Hughes Medical Institute.

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