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Protocols

BBT specifications

Information


Unique identifier OMICS_05531
Name BBT
Alternative name BioBloom tools
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C, C++, Perl, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.1.1
Stability Stable
Requirements
GCC, Boost, zlibdev, Autotools, Google Sparsehash, sdsl-lite
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Inanc Birol
  • person_outline Justin Chu

Publications for BioBloom tools

BBT citations

 (6)
library_books

Detection and genomic characterization of a mammary like adenocarcinoma

2017
PMCID: 5701302
PMID: 28877932
DOI: 10.1101/mcs.a002170

[…] Duplicate reads were marked using Picard (v1.38, https://github.com/broadinstitute/picard). Microbial and viral integration detection analysis was done using an in-house pipeline and BioBloom Tools (BBT) (). WGS variants identified using SAMtools v0.1.7 mpileup (). The tumor and normal samples were compared with identify somatic events. SNVs were called using Strelka v0.4.62 () and mutationSeq v1 […]

call_split

Automated high throughput nucleic acid purification from formalin fixed paraffin embedded tissue samples for next generation sequence analysis

2017
PLoS One
PMCID: 5453589
PMID: 28570594
DOI: 10.1371/journal.pone.0178706
call_split See protocol

[…] ality assessment of libraries, libraries were down-sampled and duplicate marked using Picard (http://picard.sourceforge.net./). Quantification of ribosomal and mitochondrial reads was performed using BioBloom Tools []. Adapter-adapter dimers or adapter sequences at the ends of reads were quantified using Skewer []. The high coverage of the mitochondrial genome in a typical RNA-seq data together wi […]

library_books

Integrated genomic and molecular characterization of cervical cancer

2017
Nature
PMCID: 5354998
PMID: 28112728
DOI: 10.1038/nature21386

[…] pathogen detection from RNA-seq data were used. The first used the microbial detection pipeline at the British Columbia Cancer Agency’s Genome Sciences Centre (BC), which is based on BioBloom Tools (BBT, v1.2.4b1). The second used the PathSeq algorithm at the Broad Institute (BI) to perform computational subtraction of human reads followed by alignment of residual reads to a combined database of […]

library_books

ntCard: a streaming algorithm for cardinality estimation in genomics data

2017
Bioinformatics
PMCID: 5408799
PMID: 28453674
DOI: 10.1093/bioinformatics/btw832

[…] w version of our genome assembly software package, ABySS 2.0 (), to determine the values for total memory size and number of hash functions. It has been also utilized to set the Bloom filter sizes in BioBloom tools (), which is a general use fast sequence categorization tool utilizing Bloom filters. Using ntCard these tools are able to get the total number of distinct k-mers F0, as well as the num […]

library_books

Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate Producing, Clostridial Scavenger from Metagenomic Sequence Data

2016
Front Microbiol
PMCID: 4880562
PMID: 27303377
DOI: 10.3389/fmicb.2016.00783

[…] or further processing. We then removed contigs shorter than 1,000 bp and with reported coverage less than 2X. Putative contaminant sequences (i.e., those not belonging to the bins) were removed using BioBloom tools version 2.0.6 (), trained with either the original MGS gene bin or with the corresponding published assembly, if available. We continued removing putative contaminants using CheckM vers […]

library_books

Draft Genome Sequences of 24 Microbial Strains Assembled from Direct Sequencing from 4 Stool Samples

2015
Genome Announc
PMCID: 4447905
PMID: 26021920
DOI: 10.1128/genomeA.00526-15

[…] ng and assembly, we iteratively mapped the reads onto the MetaHIT metagenomic species references () using BWA 0.7.10 (), assembled each bin using SPAdes 3.5.0 (), and removed extraneous contigs using BioBloom Tools 2.0.6 (). For the de novo binning and assembly, we assembled the whole metagenome using Ray 2.3.1 (), for a total of 2.1 Gbp assembled into 1,748,414 contigs, with an N50 of 40,874 bp. […]

Citations

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BBT institution(s)
Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
BBT funding source(s)
Supported by Genome Canada, British Columbia Cancer Foundation and Genome British Columbia.

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