Redkmer specifications

Unique identifier:
OMICS_22925
Interface:
Command line interface
Input data:
A whole genome sequencing data based on long single-molecule (male-only or mixed sex samples and reads must be self-error corrected) and short reads from both male and female samples independently and a file with the mitochondrial reference genome.
Output data:
A file with kmer results, candidates and data for plotting
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
1.0
Maintained:
Yes
Software type:
Pipeline/Workflow
Restrictions to use:
None
Input format:
FASTA+FASTQ
Output format:
TXT+FASTA
Programming languages:
Assembly language, R, Shell (Bash)
Computer skills:
Advanced
Stability:
Stable

versioning

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Redkmer distribution

download

Redkmer support

Additional information

https://github.com/genome-traffic/redkmer-hpc/wiki

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Publications

Institution(s)

Department of Experimental Medicine, University of Perugia, Perugia, Italy; Department of Life Sciences, Imperial College London, London, UK

Funding source(s)

Supported by a Rita Levi Montalcini award from the Ministry Education, University and Research (MIUR – D.M. no. 79 04.02.2014), the BBSRC under the research grant BB/P000843/1, in part by a grant from the Foundation for the National Institutes of Health through the Vector-Based Control of Transmission: Discovery Research (VCTR) program of the Grand Challenges in Global Health initiative of the Bill & Melinda Gates Foundation and by the European Research Council under the European Union’s Seventh Framework Programme ERC grant no. 335724.

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