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MyCC specifications

Information


Unique identifier OMICS_11820
Name MyCC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Yu-Chieh Liao <>

Publication for MyCC

MyCC in publications

 (4)
PMCID: 5955933
PMID: 29581530
DOI: 10.1038/s41396-018-0098-9

[…] assembled using metaspades [] with the following parameters (--only-assembler -k 31,41,51,61,71,81,91,101,111,121). assembled scaffolds ≥ 2500 bp were binned separately using metabat v0.26.1 [] and mycc []. results of two binning methods for each sample were combined and a non-redundant set of bins was chosen. the acquired genomes were curated manually with two approaches: (1) using the checkm […]

PMCID: 5790920
PMID: 29382738
DOI: 10.1128/mBio.02345-17

[…] of 10 steroid degradation protein families analyzed. download fig s2, pdf file, 0.1 mb., tetranucleotide frequency-based genome binning of metagenomes with high steroid degradation potential using mycc () produced 1,332 bins with genome contamination below 10% and completeness of more than 25%. forty-nine of these metagenome-assembled genomes (mags) from 33 metagenomes were predicted to encode […]

PMCID: 5421315
PMID: 28453654
DOI: 10.1093/gbe/evx082

[…] 00 bp, totaling 7.31 mb. redundant contigs were removed using the reduction step in the redundans pipeline (). for binning based on genomic signatures, marker genes, and contig coverage, the software mycc () was used with default parameters. as low coverage and short contigs are known to be error-prone, contigs with a length <1 kb and average coverage <3 were discarded from the binning. the […]

PMCID: 5148923
PMID: 27980708
DOI: 10.1016/j.csbj.2016.11.005

[…] of extra knowledge in the form of linkage of contigs provided by pair-end reads, and co-alignment to reference genomes into the binning method in order to enhance the binning performance., mycc uses k-mer frequency vectors with optional addition of coverage information, which makes the method either hybrid, or composition based, in case that the coverage information is not available. […]


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MyCC institution(s)
Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
MyCC funding source(s)
This work was supported by grants (PH-104-PP-05 and PH-104-SP-03) from the National Health Research Institute, Taiwan, and a research grant (MOST-104-2320-B-400-021-MY2) from the Ministry of Science and Technology, Taiwan.

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