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.

TranscriptSimulator 0.7 – Simulate Transcriptome Next-gen Reads, including 454 and Illumina

TranscriptSimulator 0.7

:: DESCRIPTION

TranscriptSimulator: Simple text-based, next-gen output simulator. Specifically designed to simulate transcriptome next-gen reads, including 454 and Illumina. Uses a model to simulate transcription followed by simulated sequencing using various customizable parameters. Uses a nucleotide gene set as a template (e.g. in silico predicted gene set). Version 0.70 has simulated SNPs/Indels with an improved model.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

TranscriptSimulator

:: MORE INFORMATION

NoDe – Error-correcting Algorithm for 454 Pyrosequencing Reads

NoDe

:: DESCRIPTION

NoDe (Noise Detector) is a new error correction algorithm which was trained to identify those positions in 454 sequencing reads that are likely to have an error, and subsequently clusters those error-prone reads with correct reads resulting in error-free representative read.

::DEVELOPER

The Bioinformatics team of the Microbiology Unit, SCK.CEN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

NoDe

:: MORE INFORMATION

Citation:

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads.
Mysara M, Leys N, Raes J, Monsieurs P.
BMC Bioinformatics. 2015 Mar 15;16(1):88.

InDelFixer 1.1 – An Insertion and Deletion Fixing Aligner for 454, Illumina and PacBio

InDelFixer 1.1

:: DESCRIPTION

InDelFixer is a java program to remove frame shift causing insertions or deletions from next-generation sequencing data.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

InDelFixer

:: MORE INFORMATION

Mason 0.1.2 – Read Simulator software for Illumina, 454 and Sanger reads

Mason 0.1.2

:: DESCRIPTION

Mason is a read simulator software for Illumina, 454 and Sanger reads. Its features include position specific error rates and base quality values. For Illumina reads, we give a comprehensive analysis with empirical data for the error and quality model. For the other technologies, we use models from the literature. It has been written with performance in mind and can sample reads from large genomes.

::DEVELOPER

Manuel Holtgrewe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX /Windows

:: DOWNLOAD

Mason

:: MORE INFORMATION

Citation

Holtgrewe, M. (2010).
Mason – a read simulator for second generation sequencing data.
Technical Report TR-B-10-06, Institut für Mathematik und Informatik, Freie Universität Berlin.

PyroCleaner 1.3 – Clean 454 Pyrosequencing Reads in order to ease the Assembly Process

PyroCleaner 1.3

:: DESCRIPTION

The pyrocleaner is intended to clean the reads included in the sff file in order to ease the assembly process. It enables filtering sequences on different criteria such as length, complexity, number of undetermined bases which has been proven to correlate with poor quality and multiple copy reads. It also enables to clean paired-ends sff files and generates on one side a sff with the validated paired-ends and on the other the sequences which can be used as shotgun reads.

::DEVELOPER

the bioinformatic plateforms of Genotoul.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
NCBI_blast
sff_extract

:: DOWNLOAD

PyroCleaner

:: MORE INFORMATION

Citation

Mariette J, Noirot C, Klopp C.
Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool.
BMC Research Notes 2011, 4:149

ReadSim 0.12 – Simulator for Sanger and 454 Sequencing

ReadSim 0.12

:: DESCRIPTION

ReadSim is a sequencing simulator that simulates the sequencing of reads both for Sanger and pyro-sequencing, optionally involving mate-pairs.

::DEVELOPER

Darwin Rocks Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java

:: DOWNLOAD

ReadSim

:: MORE INFORMATION

ReadSim is no longer maintained. All concepts of ReadSim are integrated into our new software MetaSim.