libCSAM – Lossy Compression of Quality Scores in Genomic data

libCSAM

:: DESCRIPTION

libCSAM will contain several C++ codes for compress,decompress, and access each of the fields of any SAM format file.

::DEVELOPER

Rodrigo Cánovas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 libCSAM

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 2.
Lossy compression of quality scores in genomic data.
Cánovas R1, Moffat A, Turpin A.

RAUR – Re-alignment of unmapped Reads with base Quality Score

RAUR

:: DESCRIPTION

RAUR is to re-align the reads that can not be mapped by alignment tools. It takes advantages of the base quality scores (reported by the sequencer) to figure out the longest segment of a read with at most K low quality bases. Combined with an alignment tool (like bwa or bowtie2), RAUR re-align the trimmed reads.

::DEVELOPER

CSU-Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Perl

:: DOWNLOAD

 RAUR

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2015 Mar 18;16 Suppl 5:S8. doi: 10.1186/1471-2105-16-S5-S8. Epub 2015 Mar 18.
Re-alignment of the unmapped reads with base quality score.
Peng X, Wang J, Zhang Z, Xiao Q, Li M, Pan Y.

QVZ / QVZ2 0.1 – A Lossy Compressor for Quality Scores in Genomic Data

QVZ / QVZ2 0.1

:: DESCRIPTION

QVZ (Quality Value Zip) is a lossy compression algorithm for storing quality values associated with DNA sequencing.

::DEVELOPER

Greg Malysa, Mikel Hernaez, Idoia Ochoa, Milind Rao, and Karthik Ganesan at Stanford University.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 QVZ / QVZ2

:: MORE INFORMATION

Citation

QVZ: lossy compression of quality values.
Malysa G, Hernaez M, Ochoa I, Rao M, Ganesan K, Weissman T.
Bioinformatics. 2015 May 28. pii: btv330.

Quartz 0.2 – de novo Quality Score Compression tool

Quartz 0.2

:: DESCRIPTION

Quartz (QUAlity score Reduction at Terabyte scale) is an efficient de novo quality score compression tool based on traversing the k-mer landscape of NGS read datasets.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Quartz

:: MORE INFORMATION

Citation:

Nat Biotechnol, 33 (3), 240-3 Mar 2015
Quality Score Compression Improves Genotyping Accuracy
Y William Yu, Deniz Yorukoglu , Jian Peng, Bonnie Berger

CorQ 20130619 – Quality Score based Identification and Correction of Pyrosequencing Errors

CorQ 20130619

:: DESCRIPTION

CorQ (Correction through Quality) is a new algorithm which utilizes the inherent base quality in a sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion (indel) errors.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 CorQ

:: MORE INFORMATION

Citation

PLoS One. 2013 Sep 5;8(9):e73015. doi: 10.1371/journal.pone.0073015. eCollection 2013.
Quality score based identification and correction of pyrosequencing errors.
Iyer S1, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI.