BioBloomTools 2.3.3 – Fast Sequence Categorization tool utilizing Bloom filters

BioBloomTools 2.3.3

:: DESCRIPTION

BioBloom Tools (BBT) provides the means to create filters for a given reference and then to categorizes sequences. This methodology is faster than alignment but does not provide mapping locations. BBT was initially intended to be used for pre-processing and QC applications like contamination detection, but is flexible to accommodate other purposes.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

BioBloom Tools

:: MORE INFORMATION

Citation

BioBloom Tools: Fast, accurate and memory-efficient host species sequence screening using Bloom filters.
Chu J, Sadeghi S, Raymond A, Jackman SD, Nip KM, Mar R, Mohamadi H, Butterfield YS, Robertson AG, Birol I.
Bioinformatics. 2014 Aug 20. pii: btu558.

BLESS v1p02 – Bloom-filter-based Error Correction Tool for NGS reads

BLESS v1p02

:: DESCRIPTION

BLESS (BLoom-filter-based Error correction Solution for high-throughput Sequencing reads) is a novel algorithm that produces accurate correction results with much less memory compared with previous solutions.

::DEVELOPER

BLESS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GCC

:: DOWNLOAD

BLESS

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1354-62. doi: 10.1093/bioinformatics/btu030. Epub 2014 Jan 21.
BLESS: bloom filter-based error correction solution for high-throughput sequencing reads.
Heo Y1, Wu XL, Chen D, Ma J, Hwu WM.

BARCODE – A fast Lossless Read Compression tool based on Bloom Filters

BARCODE

:: DESCRIPTION

BARCODE achieves highly efficient compression by using a reference genome, but completely circumvents the need for alignment, affording a great reduction in the time needed to compress.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/ MacOsX
Python

:: DOWNLOAD

BARCODE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014;15 Suppl 9:S7. doi: 10.1186/1471-2105-15-S9-S7. Epub 2014 Sep 10.
Fast lossless compression via cascading Bloom filters.
Rozov R, Shamir R, Halperin E.

SBT / SSBT 0.1 – (Split) Sequence Bloom Tree

SBT / SSBT 0.1

:: DESCRIPTION

The SBT (Sequence Bloom Tree) is a method that will allow you to index a set of short-read sequencing experiments and then query them quickly for a given sequence

SSBT is a method that will allow you to index a set of short-read sequencing experiments and then query them quickly for a given sequence.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOs
GCC
Jellyfish

:: DOWNLOAD

SBT / SSBT

:: MORE INFORMATION

Citation

Brad Solomon, Carl Kingsford (2016).
Fast search of thousands of short-read sequencing experiments.
Nature Biotechnology 34:300-302.

J Comput Biol. 2018 Jul;25(7):755-765. doi: 10.1089/cmb.2017.0265. Epub 2018 Mar 12.
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees.
Solomon B, Kingsford C