Tag: Suffix Tree

Pluribus / PluribusFast – Exploring the Limits of Error Correction Using a Suffix Tree

Pluribus / PluribusFast

:: DESCRIPTION

Pluribus utilizes a suffix tree to identify and correct sequencing errors in next generation sequencing data.

PluribusFast is a more efficient implementation of the Pluribus algorithm.

::DEVELOPER

Pluribus team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • JRE

:: DOWNLOAD

 Pluribus / PluribusFast

:: MORE INFORMATION

Citation

Pluribus – Exploring the Limits of Error Correction Using a Suffix Tree.
Savel D, LaFramboise T, Grama A, Koyuturk M.
IEEE/ACM Trans Comput Biol Bioinform. 2016 Jun 29.

ERA v1 – Efficient Serial and Parallel Suffix Tree Construction

ERA v1

:: DESCRIPTION

ERA (Elastic Range), a disk-based suffix tree construction method, which works efficiently with very long strings that are much larger than the available memory.

::DEVELOPER

InfoCloud Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C Compiler

:: DOWNLOAD

 ERA

:: MORE INFORMATION

Citation:

Essam Mansour, Amin Allam, Spiros Skiadopoulos, Panos Kalnis:
ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings.
PVLDB 5(1): 49-60 (2011)

STS 1.4 – Suffix Tree Searcher

STS 1.4

:: DESCRIPTION

STS (Suffix Tree Searcher) is a Java program for building and exploring indexes of small or large amounts of DNA data. It connects to C programs that do the heavy lifting. The indexes are actually disk-resident partitioned suffix trees, and can be constructed for single or multiple DNA sequences in very flexible ways. The input format is fasta. The output is in the form of tabular results, generally showing longest common substring (LCS) matches among the input sequences. You can also search for exact and inexact occurrences of user specified strings.

::DEVELOPER

the Upton lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX
  • Java

:: DOWNLOAD

STS

:: MORE INFORMATION