NGSphy specifications

Information


Unique identifier OMICS_22076
Name NGSphy
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A NGSPhy settings file, an INDELible control file and a Newick file with single gene tree accompanied by optional files such as ancestral sequence file and reference allele file (For single gene-tree scenario) or a NGSPhy settings file, a SimPhy output accompanied by an optional reference allele file (for species tree scenario).
Input format NEWICK/FASTA
Output data NGS reads, read counts, sequence alignments, coverage variation, log files and bash scripts.
Output format FASTQ,ALN,BAM,VCF,FASTA,CSV,BASH
Operating system Unix/Linux
Programming languages Python, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.8
Stability Stable
Requirements
DendroPy, INDELible, ART, SimPhy
Source code URL https://codeload.github.com/merlyescalona/ngsphy/zip/1.0.8
Maintained Yes

Download


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Versioning


No version available

Maintainer


  • person_outline Merly Escalona

Additional information


https://github.com/merlyescalona/ngsphy/wiki

Publication for NGSphy

NGSphy institution(s)
Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain; Galicia Sur Health Research Institute, Vigo, Spain.
NGSphy funding source(s)
Supported by the Spanish government (research grants BFU2012-33038 and BFU-BFU2015-63774-P); FPI graduate fellowship BES-2013-067181 and Juan de la Cierva postdoctoral fellowship FPDI-2013-17503; and the European Research COUncil (ERC-617457-PHYLOCANCER).

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