METagenomics

1. Galaxy for Metagenomics
Padmini Ramachandran
Division of Microbiology
ORS, CFSAN, FDA

2. Galaxy Training Cluster
• Site = https://galsingtrn.galaxytrakr.org/
• Username = (gtrX or gtrXX or gtrXXX)@ggt.org
• Password = g@lt3aiN
• Test connectivity and login
• Cluster will be shutdown after GMI conference
• We will use shared data for training

3. TOOLS AVAILABLE NOW
• Metaphlan
• Kraken 2
In the works
• MITOKmer
• BacterialKmer

5. METAPHLAN
• MetaPhlAn: Metagenomic Phylogenetic Analysis
• MetaPhlAn is a computational tool for profiling the composition of microbial communities from
metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes
identified from 3,000 reference genomes, allowing:
• up to 25,000 reads-per-second (on one CPU) analysis speed (orders of magnitude faster compared to
existing methods);
• unambiguous taxonomic assignments as the MetaPhlAn markers are clade-specific;
• accurate estimation of organismal relative abundance (in terms of number of cells rather than fraction
of reads);
• species-level resolution for bacterial and archaeal organisms;
• extensive validation of the profiling accuracy on several synthetic datasets and on thousands of real
metagenomes.

6. DATASET- 12 fastq files
Quasi metagenomics-
• Naturally contaminated icecream
• 48 hour incubation – 4 hour time points
• Shotgun metagenomics
• Illumina- Miseq
• Merged reps

12. Some things to remember
• The order of merge files
• Remembering the data file number
• Merge output sample names
• Krona and heat map clustering.

13. GalaxyTrakr.org Registration
https://account.galaxytrakr.org/Account/Register

14. Thank You
FDA/CFSAN
Errol Strain
Andrea Ottesen
Jayanthi Gangiredla
Charles Strittmatter
Justin Payne
Tom Farrell
SAIC
Jimmy Sanders