Tag: SBT

HowDe-SBT 2.00.02 – Sequence Bloom Tree, supporting determined/How Split Filters

HowDe-SBT 2.00.02

:: 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.

HowDeSBT is a data structure, which uses a novel partitioning of information to reduce the construction and query time as well as the size of the index.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

HowDeSBT

:: MORE INFORMATION

Citation

Bioinformatics, 36 (3), 721-727 2020 Feb 1
Improved Representation of Sequence Bloom Trees
Robert S Harris , Paul Medvedev

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