ntCard specifications

Information


Unique identifier OMICS_14704
Name ntCard
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The set of genomic sequences.
Input format FASTA, FASTQ, SAM, BAM, GZ, BZ, ZIP
Output data The estimated frequencies of k-mers.
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes

Download


download.png
github.png
conda.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Hamid Mohamadi

Publication for ntCard

ntCard citation

library_books

ntCard: a streaming algorithm for cardinality estimation in genomics data

2017
Bioinformatics
PMCID: 5408799
PMID: 28453674
DOI: 10.1093/bioinformatics/btw832

[…] ize and number of hash functions. It has been also utilized to set the Bloom filter sizes in BioBloom tools (), which is a general use fast sequence categorization tool utilizing Bloom filters. Using ntCard these tools are able to get the total number of distinct k-mers F0, as well as the number of k-mers above a certain multiplicity threshold. The k-mer coverage histograms computed by ntCard can […]

ntCard institution(s)
Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; University of British Columbia, Vancouver, BC, Canada
ntCard funding source(s)
This work was supported by Genome Canada, Genome British Columbia, and British Columbia Cancer Foundation and partially funded by the National Institutes of Health under Award Number R01HG007182.

ntCard reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ntCard