Tag: Coral

Coral 1.4.1 – Error Correction Algorithm for Correcting reads from DNA sequencing platforms

Coral 1.4.1

:: DESCRIPTION

Coral is an error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer. Coral can utilize also bases distant from the error in the correction process because the whole read is present in the alignment. Coral is easily adjustable to reads produced by different sequencing technologies like Illumina Genome Analyzer and Roche/454 Life Sciences sequencing platforms because the sequencing error model can be defined by the user.

::DEVELOPER

Jan Schröder , Leena Salmela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Coral

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Jun 1;27(11):1455-61. Epub 2011 Apr 5.
Correcting errors in short reads by multiple alignments.
Salmela L, Schröder J.

CoRAL 1.1.1 – Classification of RNAs by Analysis of Length

CoRAL 1.1.1

:: DESCRIPTION

CoRAL is a machine learning package that can predict the precursor class of small RNAs present in a high-throughput RNA-sequencing dataset. In addition to classification, it also produces information about the features that are most important for discriminating different populations of small non-coding RNAs.

::DEVELOPER

Wang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • libgsl
  • bigWigToBedGraph (a UCSC kent utility)
  • bedtools
  • samtools
  • RNAfold
  • ruby
  • R package

:: DOWNLOAD

 CoRAL

:: MORE INFORMATION

Citation

Leung,Y.Y., Ryvkin,P., Ungar,L., Gregory,B.D., and Wang, L.-S. (2013)
CoRAL: Predicting non-coding RNAs from small RNA-sequencing.
Nucl. Acids Res. (2013) doi: 10.1093/nar/gkt426