MCSC specifications

Information


Unique identifier OMICS_14439
Name MCSC
Alternative name Model-based Categorical Sequence Clustering
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Output data The n clusters, tab with statistic on all clusters, plot of the clustering, decontaminated fasta file
Output format FASTA, TSV, JPEG
Operating system Unix/Linux
Programming languages Perl, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
DIAMOND blast, Uniref90 database, Uniref100 taxlist
Maintained Yes

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No version available

Documentation


Maintainer


  • person_outline Benjamin Mimee

Publication for Model-based Categorical Sequence Clustering

MCSC citation

library_books

A software tool ‘CroCo’ detects pervasive cross species contamination in next generation sequencing data

2018
BMC Biol
PMCID: 5838952
PMID: 29506533
DOI: 10.1186/s12915-018-0486-7

[…] , Anvi’o [], first automatically bins contigs based on read coverage and/or k-mer frequencies, then identifies the contaminant bins. Lastly, the algorithm Model-based Categorical Sequence Clustering (MCSC) [] uses a clustering method based on the frequent patterns observed in the sequences (divisive hierarchical clustering) and then identifies the contaminant clusters by blasting against the UniRe […]

MCSC institution(s)
Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada; Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada; Département d’informatique, Université de Sherbrooke, Sherbrooke, QC, Canada
MCSC funding source(s)
This work was supported by Agriculture and Agri-Food Canada (AAFC) and the United States Department of Agriculture (USDA).

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