Parsnp pipeline

Parsnp specifications


Unique identifier OMICS_21461
Name Parsnp
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data a directory of files to be aligned
Input format MultiFASTA
Output data A single binary file encoding the reference genome, annotations, alignment, variants, and tree.
Output format BED, GenBank, FASTA, MAF, Newick, VCF, XMFA.
Operating system Unix/Linux, Mac OS
Programming languages C++, Python, Shell (Bash)
Parallelization OpenMP
Computer skills Advanced
Version 1.2
Stability Stable
Requirements gcc compiler, OpenMP
Maintained Yes



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  • person_outline Todd J. Treangen <>

Additional information

Publication for Parsnp

Parsnp citation

PMCID: 5876403

[…] chromosome, plasmids and all the raw reads are deposited under the project with accession number ers726104. for plasmids, the core genome single nucleotide polymorphisms (snps) was identified using parsnp27. the virulence and antibiotic resistance genes were identified by blastp against the vfdb and card respectively28,29., galleria mellonella larvae were reared on an artificial diet (22% maize […]

Parsnp institution(s)
National Biodefense Analysis and Countermeasures Center, MD, USA
Parsnp funding source(s)
Supported by an Agreement (No. HSHQDC-07-C-00020) awarded by the Department of Homeland Security Science and Technology Directorate (DHS/S&T) for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC); and a Federally Funded Research and Development Center.

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