What will be covered?

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3 What will be covered? 1. Annotation overview 2. Using the RAST family for genome annotation: Optimizing RAST for phages Command line/ Batch options 3. Introducing PATRIC and resources in development Therapeutic phage database Assembly Variation analysis Metagenome binning

4 Subsystems-based tools & SEED Aziz RK,, et al. (2012) PLoS ONE 7(10): e doi: /journal.pone July 2018 Phage Genomics - VoM 2018

5 SEED Subsystems: Main concept One genome All genomes

6 SEED Subsystems: Main concept One genome All genomes Subsystems-based technologies were developed in the SEED with the view that the interpretation of one genome can be made more efficient and consistent if hundreds of genomes are simultaneously annotated in one subsystem at a time

7 What is a subsystem? A subset of functional roles studied across genomes A spreadsheet where: each row represents a genome each column represents a functional role/ feature/ protein different patterns = variants Function 1 Function 2 Function n Genome a Genome b Genome z 9 July 2018 Phage Genomics - VoM 2018

8 RAST (

9 RAST: automated annotation

10 Subsystems-based tools (Extended RAST family) (At least) Five ways to annotate a genome via RAST: RAST ( annotates online, saves your genome on server Use your favorite gene caller then upload gbk file to RAST myrast (local) uses the server but you can edit offline) RASTtk (second-generation RAST) modular batch upload PATRIC New Coming Soon: new gene caller Phanotator

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13 RASTtk (RAST toolkit)

14 RASTtk command-line

15 RAST Video demos available Find & watch:

16 How to? TUTORIAL 1: USING RAST FOR PHAGE ANNOTATION 9 July 2018 Phage Genomics - VoM 2018

17 What do you need to annotate your genome? A sequenced genome Format: fasta or genbank (.gbk) A RAST username and password You can find some test data (T4, T7, Lambda) at

18 1. Optimizing RASTtk for phage

19 1. Optimizing RASTtk for phage

20 1. Optimizing RASTtk for phage

21 1. Optimizing RASTtk for phage

22 1. Optimizing RASTtk for phage

23 1. Optimizing RASTtk for phage?

24 1. Optimizing RASTtk for phage?

25 1. Optimizing RASTtk for phage

26 1. Optimizing RASTtk for phage

27 1. Optimizing RASTtk for phage

28 2. Command-line RASTtk (Batch option) Where? On IRIS ( docs/invocation/iris/iris.html) On your desktop (Download RASTtk)

29 2. Command-line RASTtk (Batch option) How? The key is to convert each contigs file (fasta) to so-called Genome-typed object GTO Once you have GTOs for all your genomes, you can run a couple of commands to annotate each of them OR put them in a folder and annotate in batch

30 2. Command-line RASTtk (Batch option) Commands: o rast-create-genome! rast-create-genome --scientific-name Enterophage Lambda" --genetic-code 11 --domain Virus --contigs lambda.fasta > lambda.gto! o rast-process-genome! o rast-process-genome-batch! o rast-export-genome! Details on or follow link from:

31 Next à PATRIC (patricbrc.org)

32 Subsystems-based tools COMMUNITY STANDARDS, METADATA AND ANNOTATIONS

33 SEED allows continuous annotation SEED Viewer New Genomes RAST SEED Subsystems Editor Subsystems Genomes 9 July 2018 Phage Genomics - VoM 2018

34 SEED allows community annotation

35 Annotations will improve only if YOU help