This is the Linux app named SuRankCo to run in Linux online whose latest release can be downloaded as surankco_r5.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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SuRankCo to run in Linux online
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DESCRIPTION
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.
Audience
Science/Research
User interface
Command-line
Programming Language
Java, S/R
This is an application that can also be fetched from https://sourceforge.net/projects/surankco/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
