Redkmer specifications

Information


Unique identifier OMICS_22925
Name Redkmer
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
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.
Input format FASTA+FASTQ
Output data A file with kmer results, candidates and data for plotting
Output format TXT+FASTA
Operating system Unix/Linux
Programming languages Assembly language, R, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Additional information


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

Publication for Redkmer

Redkmer institution(s)
Department of Experimental Medicine, University of Perugia, Perugia, Italy; Department of Life Sciences, Imperial College London, London, UK
Redkmer 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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