Tag: Short Read

SHREC 2.2 – Short Read Error Correction

SHREC 2.2

:: DESCRIPTION

SHREC is a new algorithm for correcting errors in short-read data that uses a generalized suffix trie on the read data as the underlying data structure. Our results show that the method can identify erroneous reads with sensitivity and specificity of over 99% and 96% for simulated data with error rates of up to 3% as well as for real data. Furthermore, it achieves an error correction accuracy of over 80% for simulated data and over 88% for real data. These results are clearly superior to previously published approaches.

::DEVELOPER

Jan Schröder

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SHREC

:: MORE INFORMATION

Citation:

Jan Schröder, Heiko Schröder, Simon J. Puglisi, Ranjan Sinha, and Bertil Schmidt,
SHREC: A short-read error correction method,
Bioinformatics, 2009 25(17):2157-2163.

FreClu – Efficient Frequency-based De novo Short Read Clustering

FreClu

:: DESCRIPTION

FreClu: Efficient Frequency-based De novo Short Read Clustering — de novo clustering

::DEVELOPER

Morishita Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java 

:: DOWNLOAD

 FreClu

:: MORE INFORMATION

Citation

Wei Qu, Shin-ichi Hashimoto and Shinichi Morishita
Efficient frequency-based de novo short read clustering for error trimming in next-generation sequencing.
Genome Res. 2009. 19:1309-1315

 

Edena v3.131028 – De Novo Short Reads Assembler

Edena v3.131028

:: DESCRIPTION

Edena is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer

::DEVELOPER

D. Hernandez @ The Genomic Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Edena

:: MORE INFORMATION

Citation:

Hernandez D, François P, Farinelli L, Osterås, Schrenzel J.
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.
Genome Research. 18:802-809, 2008.

YASRA 2.33 – Yet Another Short Read Assembler

YASRA 2.33

:: DESCRIPTION

YASRA performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced.

::DEVELOPER

Aakrosh Ratan (ratan@bx.psu.edu) at Miller Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 YASRA

:: MORE INFORMATION

Citation

Ratan, Aakrosh
Assembly algorithms for next-generation sequencing data.

Srfim 0.0-95 – Short-Read Filtering and Intensity-Modeling

Srfim 0.0-95

:: DESCRIPTION

Srfim does model-based quality assessment and base-calling for Illumina GA second-generation sequencing data.

::DEVELOPER

Héctor Corrada Bravo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 Srfim

:: MORE INFORMATION

Citation:

H. Corrada Bravo, R.A. Irizarry.
“Model-based quality assessment and base-calling for second-generation sequencing data” (Novmeber 2009).
Biometrics. Published online before print, Novemeber 13, 2009. doi10.1111/j.1541-0420.2009.01353.x

CompMap – Compressive Short Read Mapping

CompMap

:: DESCRIPTION

CompMap is a reference-based compression program to speed up read mapping to related reference sequences. CompMap is designed to eliminate repeat subsequences based on reference-base compression in the input curating database, which could contain complete genomes, plasmids, and/or other sequences.

::DEVELOPER

Zexuan ZHU

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

  CompMap

:: MORE INFORMATION

Citation:

CompMap: a reference-based compression program to speed up read mapping to related reference sequences.
Zhu Z, Li L, Zhang Y, Yang Y, Yang X.
Bioinformatics. 2014 Oct 4. pii: btu656

FLASH 1.2.11 – Fast Length Adjustment of SHort reads

FLASH 1.2.11

:: DESCRIPTION

FLASH (Fast Length Adjustment of SHort reads) is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.

::DEVELOPER

Center for Computational Biology , Johns Hopkins University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 FLASH

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Nov 1;27(21):2957-63. Epub 2011 Sep 7.
FLASH: fast length adjustment of short reads to improve genome assemblies.
Tanja Magoč, Salzberg SL.

Reptile 1.1 – Short Read Error Correction

Reptile 1.1

:: DESCRIPTION

Reptile (Representative tiling) corrects sequencing errors in short reads (32bp ~ 150bp) generated by next-gen sequencing platforms, e.g. Illumina.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • Perl

:: DOWNLOAD

 Reptile

:: MORE INFORMATION

Citation

X. Yang, K. Dorman and S. Aluru,
“Reptile: Representative tiling for short read error correction”,
Bioinformatics, 26(20), 2526-2533, 2010.

proovread 2.14.1 – Large-scale high accuracy PacBio Correction through iterative Short Read Consensus.

proovread 2.14.1

:: DESCRIPTION

proovread is a hybrid correction pipeline for SMRT reads, which can be flexibly adapted on existing hardware and infrastructure from a laptop to a high performance computing cluster.

::DEVELOPER

Department of Bioinformatics, University of Würzburg,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux  / MacOsX
  • SHRiMP2
  • bash version 4 or above

:: DOWNLOAD

 proovread

 :: MORE INFORMATION

Citation:

proovread: large-scale high accuracy PacBio correction through iterative short read consensus.
Hackl T, Hedrich R, Schultz J, Förster F.
Bioinformatics. 2014 Jul 10. pii: btu392.

BWBBLE – Short Read Alignment with Populations of Genomes

BWBBLE

:: DESCRIPTION

BWBBLE performs short-read alignment to a population of genomes represented by a reference multi-genome.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • C Compiler

:: DOWNLOAD

 BWBBLE

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):i361-70. doi: 10.1093/bioinformatics/btt215.
Short read alignment with populations of genomes.
Huang L, Popic V, Batzoglou S.