SuRankCo

SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.

For more details about SuRankCo and its functioning, please see

"SuRankCo: Supervised Ranking of Contigs in de novo Assemblies"
Mathias Kuhring, Piotr Wojtek Dabrowski, Andreas Nitsche and Bernhard Y. Renard
(http://www.biomedcentral.com/1471-2105/16/240/abstract)

PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo.

Update Jun2015:
* Minor changes to enable BAM support.
Update Feb2014:
* Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL).
NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet.

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License

BSD License

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Additional Project Details

Operating Systems

Linux, Mac

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Java, S/R

Related Categories

Java Bio-Informatics Software, Java Machine Learning Software, S/R Bio-Informatics Software, S/R Machine Learning Software

Registered

2013-12-06

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