Tools

More than 200 tools are automatically integrated in the custom Galaxy instance during its deployment. They were chosen for their use in exploitation of microbiota data, and are hierarchically organized (into sections and subsection) to guide users and help them to choose the best tools for a specific analysis.

• File and meta tools
  • Data retrieval
  • Text manipulation
  • Sequence file manipulation
  • BAM/SAM file manipulation
  • BIOM file manipulation
• Genomics tools
  • Quality control
  • Clustering
  • Sorting and Prediction
  • Similarity search and alignment
  • Mapping
• Microbiota dedicated tools
  • Metagenomics data manipulation
  • Assembly
  • Metataxonomic sequence analysis
  • Taxonomy assignation on WGS sequences
  • Metabolism assignation
  • Combination of functional and taxonomic results

These tools come with databases, which are automatically downloaded and configured during deployment of ASaiM Galaxy instance.

Name	Version	Comments
SILVA	119	Reduced with HMMER 3.1b1 and SumaClust v1.0.00 and formatted for SortMeRNA
ChocoPhlAn	0.1.1	Microbial pangenomes
UniRef50		Filtered with Diamond to be HUMAnN2 compatible
MetaPhlAn2	2.2.5	Unique clade-specific marker genes identified from ≃ 17,000 reference genomes