PanPhlAn pipeline

PanPhlAn specifications

Information


Unique identifier OMICS_11368
Name PanPhlAn
Alternative name Pangenome-based Phylogenomic Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements Bowtie2, Samtools
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline PanPhlAn Team <>

Publication for Pangenome-based Phylogenomic Analysis

PanPhlAn IN pipelines

 (5)
2018
PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] results were also similar across platforms. each platform correctly identified the strains present in the mock community, but accuracy was improved slightly with greater sequencing depth. notably, panphlan detected the dominant strains in each kefir sample above 500,000 reads per sample. again, the outputs from functional profiling analysis using super-focus were generally accordant […]

2018
PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] different approaches, but it does further emphasise that results obtained using different methods cannot be directly compared., next, we compared the results of strain-level analysis using panphlan, and we found that all three sequencers correctly identified the analysed strains from the mock community sample. similarly, the three platforms each indicated that the l. kefiranofaciens […]

2018
PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] that the l. kefiranofaciens and l. mesenteroides strains detected in the kefir samples were most closely related to l. kefiranofaciens gcf_001434195 and l. mesenteroides gcf_000447945, respectively. panphlan was significantly less accurate when utilising data generated by the miseq compared to either nextseq or proton data, suggesting that sequencing depth affected strain-level analysis. […]

2018
PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] either nextseq or proton data, suggesting that sequencing depth affected strain-level analysis. we subsequently confirmed this by randomly subsampling kefir sequencing reads which demonstrated that panphlan failed to detect l. kefiranofaciens gcf_001434195 or l. mesenteroides gcf_000447945 a subset of kefir samples below 500,000 reads per sample using any sequencer. similarly, and as expected, […]

2017
PMCID: 5704459
PMID: 29183332
DOI: 10.1186/s13073-017-0490-5

[…] profiled with metaphlan2 and functionally profiled using humann2. differentially abundant species were identified using maaslin and strain-specific pangenome haplotypes were analyzed using panphlan., we found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the ibd gut. we also detected dramatic, yet transient, […]

PanPhlAn institution(s)
Centre for Integrative Biology, University of Trento, Trento, Italy; Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, USA; Department of Pediatrics, Perinatal Institute, Cincinnati, OH,USA
PanPhlAn funding source(s)
This work was supported by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract number HHSN272200900018C. The work was also supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement number PCIG13-GA-2013-618833, by startup funds from the Centre for Integrative Biology, University of Trento, by MIUR “Futuro in Ricerca” RBFR13EWWI_001, by the Fondazione Caritro–2013 and by ‘Terme di Comano’.

PanPhlAn reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PanPhlAn