HECTOR 1.0 – A Parallel Homopolymer Spectrum based 454 Error Corrector

HECTOR 1.0

:: DESCRIPTION

HECTOR is a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. In this algorithm, for the first time we have investigated a novel homopolymer spectrum based approach to handle homopolymer insertions or deletions, which are the dominant sequencing errors in 454 short-reads.

::DEVELOPER

HECTOR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

HECTOR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 May 6;15(1):131. [Epub ahead of print]
HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data.
Wirawan A, Harris RS, Liu Y, Schmidt B, Schröder J.

FindTail 1.01 – Accurate Detection of Poly(A)/(T) tails and other Homopolymer in RNA-Seq and ESTs

FindTail 1.01

:: DESCRIPTION

Implemented in C++, FindTail first detects all perfect poly(A) tracts (or homopolymers)in a sequence. Starting with the first tract, FindTail then determines whether the downstream tracts can be merged to form a longer poly(A) fragment using an adjustable gap. After the merging step, it calculates the identity for all resultant poly(A) fragments and remaining tracts, and filter them using an adjustable minimum identity. Finally, the poly(A) length is calculated and filtered by an adjustable minimum length.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX/Windows
C++ Compiler

:: DOWNLOAD

FindTail

:: MORE INFORMATION

HAXAT 1.04 – Homopolymer Aware Cross Alignment Tool

HAXAT 1.04

:: DESCRIPTION

HAXAT uses a novel dynamic programming algorithm for solving the optimal local alignment between a 454 nucleotide and a protein sequence by allowing frame-shifts, guided by 454 flowpeak values.

::DEVELOPER

IFM Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

HAXAT

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 12;13:230. doi: 10.1186/1471-2105-13-230.
Highly improved homopolymer aware nucleotide-protein alignments with 454 data.
Lysholm F.