QuicK-mer protocols

QuicK-mer specifications

Information


Unique identifier OMICS_10300
Name QuicK-mer
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data QuicK-mer supports both FASTQ and BAM format as input.
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements Jellyfish, matplotlib, samtools
Maintained Yes

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Maintainer


  • person_outline Jeffrey Kidd <>

Publication for QuicK-mer

QuicK-mer IN pipelines

 (2)
2016
PMCID: 4987114
PMID: 27358426
DOI: 10.1093/gbe/evw150

[…] of amplicons, but additionally provide a unique number for each amplicon family (see supplementary table s2, supplementary material online). we assessed copy number of each amplicon family using quick-mer, a novel pipeline for paralog-specific copy-number analysis. briefly, quick-mer utilizes the jellyfish-2 (marcais and kingsford 2011) program to efficiently tabulate the depth of coverage […]

2016
PMCID: 4987114
PMID: 27358426
DOI: 10.1093/gbe/evw150

[…] (see supplementary table s2, supplementary material online). we assessed copy number of each amplicon family using quick-mer, a novel pipeline for paralog-specific copy-number analysis. briefly, quick-mer utilizes the jellyfish-2 (marcais and kingsford 2011) program to efficiently tabulate the depth of coverage of a predefined set of k-mer sequences (here, k = 30) in a set of sequencing […]

QuicK-mer institution(s)
Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
QuicK-mer funding source(s)
This work has been supported by the National Institutes of Health (grant number DP5OD009154 and R01GM103961).

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