diff --git a/README.md b/README.md index fb941e0..75c9217 100644 --- a/README.md +++ b/README.md @@ -10,12 +10,12 @@ microbial population studies. PanPhlAn is written in Python and covers the three main tasks: -* `panphlan_pangenome_generation.py`, to create the pangenome database of a bacterial species - [→ read more](https://bitbucket.org/CibioCM/panphlan/wiki/panphlan_pangenome_generation) -* `panphlan_map.py`, to profile each metagenomic sample by mapping it against the species specific database - [→ read more](https://bitbucket.org/CibioCM/panphlan/wiki/panphlan_map) -* `panphlan_profile.py`, to merge and process the mapping results for getting the final gene presence/absence and transcriptional matrices - [→ read more](https://bitbucket.org/CibioCM/panphlan/wiki/panphlan_profile) +* `panphlan_pangenome_generation.py`, to create the pangenome database of a bacterial species + [read more](https://github.com/SegataLab/panphlan/wiki/Pangenome-generation) +* `panphlan_map.py`, to profile each metagenomic sample by mapping it against the species specific database + [read more](https://github.com/SegataLab/panphlan/wiki/PanPhlAn-mapping) +* `panphlan_profile.py`, to merge and process the mapping results for getting the final gene presence/absence and transcriptional matrices + [read more](https://github.com/SegataLab/panphlan/wiki/PanPhlAn-profiling) @@ -25,14 +25,14 @@ PanPhlAn runs under Ubuntu/Linux and requires the following software tools to be * Samtools * Python 3.x (including the Biopython module) -For more information, see our wiki [→ Download and Installation](https://bitbucket.org/CibioCM/panphlan/wiki/Download_and_Installation). +For more information, see our wiki [Download and Installation](https://github.com/SegataLab/panphlan/wiki#download-the-panphlan-software). ## Contact & User support ## -[→ User Tutorial](https://bitbucket.org/CibioCM/panphlan/wiki) +A [user tutorial](https://github.com/SegataLab/panphlan/wiki/Tutorial) is available on the [PanPhlAn wiki](https://github.com/SegataLab/panphlan/wiki). For help, use also the [bioBakery help forum](https://forum.biobakery.org/). + The PanPhlAn software team: [Matthias Scholz](http://www.matthias-scholz.de/) (algorithm design), [Thomas Tolio](https://www.linkedin.com/in/thomastolio) (programmer), Leonard Dubois and [Nicola Segata](http://segatalab.cibio.unitn.it/) (principal investigator). -For help, use the [bioBakery help forum](https://forum.biobakery.org/). ----