ParaSite Ensembl Genomes and UCSC Assembly Hub WormBase Workshop International Worm Meeting 2015

1. WormBase beyond www.wormbase.org
WormBase ParaSite
• New home for parasitic worm genomes in WormBase
UCSC WormBase assembly hub
• View current WormBase data on UCSC genome browser

2. WormBase ParaSite
Motivation
• Many (100s) of parasitic nematode genome sequences available/iminent
• Helminth genomes scattered across a number of resources
• Much of data is “draft” quality
Introducing WormBase ParaSite (parasite.wormbase.org)
• Consistent, integrated access to hundreds of parasitic nematode draft genomes
• Encompass all parasitic worms (i.e. nematodes and flatworms)

3. WormBase ParaSite genomes (v2)
Nematodes
• 63 species (70 genomes)
• Clade I – 7 species (9)
• Clade III – 22 species (24)
• Clade IV – 16 species (16)
• Clade V - 18 species (21)
• Largest and smallest
• Teladorsagia circumcincta (700 Mb)
• Parastrongyloides trichosuri (42 Mb)
Platyhelminthes
• 25 species (26 genomes)
• Cestodes – 12 species
• Trematodes – 11 species
• Other– 2 species
• Largest and smallest
• Spirometra erinaceieuropaei (1250 Mb)
• Hydatigera taeniaeformis (100 Mb)
Orthologs and paralogs
•Ensembl “Compara” protein-tree pipeline
•118 genomes
• 9 additional nematode genomes (free living)
• 13 comparator genomes
• Including human, mouse, zebrafish
•~150,000 protein multiple alignments
•~1000 CPU days

4. http://parasite.wormbase.org

5. http://parasite.wormbase.org

6. ParaSite Downloads

7. ftp://ftp.wormbase.org/pub/wormbase/parasite
• Consistent file naming and data organisation
• Genome project (NCBI BioProject) disambiguation
• Files for each genome
• Genome fasta(s)
• Protein fasta
• Transcript fasta
• Annotation GFF3

8. http://parasite.wormbase.org

9. ParaSite Mart
• Table-based data-mining tool
• Like WormMine, but different interface
• Complementary to WormMine
•Less depth for C. elegans, but…
•Comprehensive species set (all nematode genomes)
•Some additional functionality

10. ParaSite Mart - orthologs

11. ParaSite Mart – sequence extraction

12. The UCSC WormBase genome Hub
Background
● Many researchers like the UCSC genome browser
○ Familiar interface
○ Comparative genomics (alignments / conservation)
● Worm data at UCSC is 5 years out of date
UCSC hubs
● A new mechanism for remote hosting of collections of genome browser tracks
● Emerging standard for cross-browser compatibility
● The WormBase hub
○ View up-to-date WormBase data on UCSC!
○ View some data not viewable anywhere else: genomic alignments

13. Nematode genomic alignments
Progressive Cactus (Nguyen et al, 2014)
• New tool (UCSC) for genome multiple alignments (100s genomes)
• Creates “virtual” ancestor genomes
• Output = HAL file (HDF5 database)
WormBase cactus alignments
• 29 nematode genomes (more in future)
• Viewable on UCSC browser (“SNAKE” tracks)

14. UCSC
Production Hub
http://ftp.ebi.ac.uk/pub/databases/wormbase/releases/current-production-release/COMPARATIVE_ANALYSIS/hub/hub.txt

15. UCSC
New Dropdowns:
● Nematodes
● core genomes
● WormBase
assembly
identifiers
Search:
● seq. names
● WBGeneIDs
● gene symbols

16. UCSC
Release Tracks:
● transcripts
● current + reference
● pseudogenes
● ncRNAs
● mRNA alignments
● WormBase links
Assembly Tracks:
● repeats
● conservation
● comparative hub

17. UCSC

18. UCSC

19. EnsEMBL (and friends)
Development Hub
http://ftp.ebi.ac.uk/pub/databases/wormbase/releases/current-development-release/COMPARATIVE_ANALYSIS/hub/parasite_hub.txt
Production Hub
http://ftp.ebi.ac.uk/pub/databases/wormbase/releases/current-production-release/COMPARATIVE_ANALYSIS/hub/parasite_hub.txt
current:
metazoa.ensembl.org
coming soon:
parasite.wormbase.org
ensembl.org
configure tracks

20. … and more
GBrowse
BioDalliance
JBrowse

21. Summary
WormBase ParaSite
• parasite.wormbase.org
• Poster 952C (Saturday)
UCSC WormBase assembly hub
• ftp.ebi.ac.uk/pub/databases/wormbase/releases/current-production-
release/COMPARATIVE_ANALYSIS/hub/hub.txt
• blog.wormbase.org
More information
• help@wormbase.org
• Come and see us for a tutorial!