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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

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Maintainer


  • person_outline Darrin Lemmer

Publication for The Northern Arizona SNP Pipeline

NASP citations

 (34)
call_split

Improved Subtyping of Staphylococcus aureus Clonal Complex 8 Strains Based on Whole Genome Phylogenetic Analysis

2018
PMCID: 5932376
PMID: 29720527
DOI: 10.1128/mSphere.00464-17
call_split See protocol

[…] vious studies selected for sequence type diversity were used to generate the CC8 phylogeny and an overall S. aureus phylogeny encompassing several clonal complexes () (, ).The bioinformatics pipeline NASP () was used to detect SNPs among genomes. In brief, reads were aligned to the finished genome FPR3757 (GenBank accession no. CP000255) using Novoalign (Novocraft.com) and SNPs were called with GA […]

library_books

Cross border outbreak of listeriosis caused by cold smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017

2017
PMCID: 5743096
PMID: 29258647
DOI: 10.2807/1560-7917.ES.2017.22.50.17-00762

[…] investigated the relatedness of outbreak isolates further by single-nucleotide polymorphisms (SNP) analysis performed by both SSI and DTU using two analysis pipelines: Northern Arizona SNP Pipeline (NASP) [] and CSI Phylogeny version 1.4 from Center for Genomics Epidemiology (CGE), DTU [] leading to the same conclusion. The SNP analysis showed a maximum of nine SNPs between any two isolates in th […]

call_split

Genomic analysis reveals different mechanisms of fusidic acid resistance in Staphylococcus aureus from Danish atopic dermatitis patients

2017
J Antimicrob Chemother
PMCID: 5890767
PMID: 29253168
DOI: 10.1093/jac/dkx481
call_split See protocol

[…] complex (CC) types were assigned from the STs using the algorithm eBURST v3 (http://eburst.mlst.net/). spa types were obtained by PCR and Sanger sequencing.SNPs in the core genome were detected using the Northern Arizona SNP pipeline (NASP) by aligning de novo assembled contigs. A random selected isolate from the study population was used as a reference. The genetic diversity among isolates was ex […]

call_split

Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White Nose Syndrome

2017
MBio
PMCID: 5727414
PMID: 29233897
DOI: 10.1128/mBio.01941-17
call_split See protocol

[…] quencing and assembly of the genome of P. destructans 20631-21, collected in New York in 2008 () (NCBI GenBank assembly accession no. GCA_001641265.1), was used as a reference for SNP discovery using the Northern Arizona SNP Pipeline (NASP) version 1.0.2 (). With NASP, Illumina paired-end reads were aligned to the reference genome with the Burrows-Wheeler Aligner () version 0.7.5a mem algorithm. S […]

library_books

Whole genome sequencing of bloodstream Staphylococcus aureus isolates does not distinguish bacteraemia from endocarditis

2017
Microb Genom
PMCID: 5729915
PMID: 29208121
DOI: 10.1099/mgen.0.000138

[…] To investigate whether single or combination of SNPs could discriminate between isolates from SAB-only and IE isolates, a total of 120 850 identified SNPs using NASP were examined. The relatedness of the isolates was inferred in a phylogeny with the IE association and most common CCs highlighted in and as a principal component analysis (PCA) plot coloured by […]

call_split

Investigation of Outbreaks of Salmonella enterica Serovar Typhimurium and Its Monophasic Variants Using Whole Genome Sequencing, Denmark

2017
PMCID: 5621559
PMID: 28930002
DOI: 10.3201/eid2310.161248
call_split See protocol

[…] de novo assembled and sequence type (ST) determined. We identified core-genome SNPs by using an in-house SNP pipeline, and we then analyzed a selected subgroup of isolates by using the SNP pipelines NASP () and CSI Phylogeny 1.2 (). A description of sequencing procedures and sequence analysis is provided (). We assessed quality of the sequences and excluded 6 isolates from the study because of po […]

Citations

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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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