PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and *in-vivo* transcriptional activity of individual strains in metagenomic samples. PanPhlAn’s ability for strain-tracking and functional analysis of unknown pathogens makes it an efficient tool for culture-free infectious outbreak epidemiology and microbial population studies.
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PanPhlAn 3 - strain detection and characterization
Pangenome-based Phylogenomic Analysis
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples. PanPhlAn’s ability for strain-tracking and functional analysis of unknown pathogens makes it an efficient tool for culture-free microbial population studies.
PanPhlAn is written in Python and covers the 4 main tasks:
panphlan_download_pangenome.py
, to download pangenome files (fasta, BowTie2 indexes and general information) for over 3,000 speciespanphlan_map.py
, to profile each metagenomic sample by mapping it against the species of interestpanphlan_profile.py
, to merge and process the mapping results in order to get the final gene presence/absence matrixpanphlan_find_gene_grp.py
, organise OPTICS clustering to find some group of gene with similar profile and assess if they could be mobile elements in the genome. Also plot the presence/absence matrix as Heatmap.
PanPhlAn runs under Ubuntu/Linux and requires the following software tools to be installed on your system:
- Bowtie2
- Samtools
- Python 3
And the following Python libraries:
- numpy
- pandas
- scipy
- sklearn (only if using
panphlan_find_gene_grp.py
)
If visualizations are made, one also needs : - matplotlib
- seaborn
For any help see the wiki or the bioBakery forum
[PanPhlAn] is a project of the Computational Metagenomics Lab at CIBIO, University of Trento, Italy
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