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Nicola Segata
Dec 27, 2012, 2:51:55 AM12/27/12
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Dear MetaPhlAn users,
in the last couple of months we have been working both on MetaPhlAn 2.0 and on several feature updates for version 1.7. Regarding the latter, the updates contained in the last released version 1.7.4 are the following:
- [1.7.4] the script metaphlan_hclust_heatmap.py in plotting_scripts/ allows you to generate hierarchical clustering and heatmap visualization of multiple MetaPhlAn profiles. See plotting_scripts/readme.txt for details
- [1.7.3] MetaPhlAn now accepts metagenomes from the standard input (when using BowTie2). When passing the input from the standard input, it is now required to specify the input type ('multifasta', 'multifastq', or 'blastout'). When using a file as input, the input type is still guessed by MetaPhlAn automatically
- [1.7.2] multiple MetaPhlAn output obtained on distinct samples can now be easily merged into a unique "microbial clades vs samples" abundance table using the merge_metaphlan_tables.py script in the "utils" folder (thanks to Tim Tickle)
- [1.7.2] the MetaPhlAn output can now be visualized with Krona and with other software supporting the PhyloXML format, using the scripts in the "conversion_scripts" folder (thanks to Daniel Brami and James Taylor)
- [1.7.1] two aspecific genes removed from the database (thanks to Nick Loman)
Let us know if you have any comment or question.
many thanks
Nicola
in the last couple of months we have been working both on MetaPhlAn 2.0 and on several feature updates for version 1.7. Regarding the latter, the updates contained in the last released version 1.7.4 are the following:
- [1.7.4] the script metaphlan_hclust_heatmap.py in plotting_scripts/ allows you to generate hierarchical clustering and heatmap visualization of multiple MetaPhlAn profiles. See plotting_scripts/readme.txt for details
- [1.7.3] MetaPhlAn now accepts metagenomes from the standard input (when using BowTie2). When passing the input from the standard input, it is now required to specify the input type ('multifasta', 'multifastq', or 'blastout'). When using a file as input, the input type is still guessed by MetaPhlAn automatically
- [1.7.2] multiple MetaPhlAn output obtained on distinct samples can now be easily merged into a unique "microbial clades vs samples" abundance table using the merge_metaphlan_tables.py script in the "utils" folder (thanks to Tim Tickle)
- [1.7.2] the MetaPhlAn output can now be visualized with Krona and with other software supporting the PhyloXML format, using the scripts in the "conversion_scripts" folder (thanks to Daniel Brami and James Taylor)
- [1.7.1] two aspecific genes removed from the database (thanks to Nick Loman)
Let us know if you have any comment or question.
many thanks
Nicola
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