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Update README.md
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leonarDubois authored Oct 9, 2020
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Expand Up @@ -11,6 +11,9 @@ pathogens makes it an efficient tool for culture-free microbial population studi
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 species

For custom pangenome generation (advanced) see the [PanPhlAn exporter](https://github.com/SegataLab/PanPhlAn_pangenome_exporter)

* `panphlan_map.py`, to profile each metagenomic sample by mapping it against the species of interest
* `panphlan_profile.py`, to merge and process the mapping results in order to get the final gene presence/absence matrix
* `panphlan_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.
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