NASP specifications

Information


Unique identifier OMICS_11190
Name NASP
Alternative name The Northern Arizona SNP Pipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTA, BAM, SAM, VCF, FASTQ, FASTQ.GZ
Output format matrix, VCF, FASTA
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.0.0
Stability Stable
Requirements SAMmtools, Trimmomatic, MUMmer
Maintained Yes

Taxon


  • Eubacteria

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Maintainer


  • person_outline Darrin Lemmer <>

NASP article

NASP citation

2017
PMCID: 5600411

[…] the reference genome of strain co92 [24] using bwa-mem [23] and snps were called with the unifiedgenotyper method in gatk [28, 29] in conjunction with the nasp pipeline (http://tgennorth.github.io/nasp) [30]. the resulting snp matrix was filtered to focus on the snps to be verified., a snp phylogeny was generated for all 773 samples using data from 42 informative snps from the 63 screened […]

NASP institution(s)
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA; Translational Genomics Research Institute, Flagstaff, AZ, USA; The George Washington University, Washington DC, USA; University of New Hampshire, Durham, NH, USA

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