1000 Insect Transcriptomes Evolution - 1KITE
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1 1KITE 1K Insect Transcriptome Evolution 1000 Insect Transcriptomes Evolution - 1KITE An Example of Handling "Big Data" Karen Meusemann, on behalf of the 1KITE Consortium CSIRO Ecosystem Sciences, Australian National Insect Collection, Canberra, Australia BIG DATA WORKSHOP, Hobart, Tasmania, Australia, September 2013
2 Motivation We want to understand the evolution of insects in all of its aspects, in particular the relationship of genomic and morphological diversification using the results of the most advanced approaches in genomic and morphological research. Leaders Xin Zhou, BGI Shenzhen Karl Kjer, Ruttgers, NJ Bernhard Misof, ZMB, ZFMK Bonn & 1KITE team
3 The 1KITE Consortium: > 70 scientists (8 nations) from molecular biology, morphology, systematics, paleontology, embryology, bioinformatics, and scientific computing.
4 1KITE Challenges Challenges I coordinate collecting of 1,000 insect species transcriptome sequencing
5 1KITE Challenges What is a transcriptome? A transcriptome contains everything that is transcribed at the time, the specimen was preserved, e.g., protein-encoding genes (Drosophila melanogaster: ~24,000 transcripts, millions of sites) large part of the genome which is important to maintain the metabolism of organisms.
6 1KITE Challenges Challenges II care about data quality analyse data using sophisticated pipelines develop new tools that can handle these data amounts [~1,000,000,000 bp) link data from non-molecular sources
7 1KITE Challenges Struck et al. (2011) 1KITE, (in prep.) x 10 by the end of 2013 ~ 900 species finished
8 1KITE Challenges Challenges III coordinate data management, data exchange, data storage and access make data and tools available coordinate collaborators, and related projects.
9 Organisation and Workflow
10 Organisation and Workflow Peter Grobe 1KITE DATABASE
11 1KITE Data Kinds of Data insect tissue, vouchers, barcodes meta-information of collected species sequence data (raw data and assemblies, and meta-information) analysed data (superalignments [ ], trees and meta-information) protocols, guidelines, READMEs
12 Collection Preservation Shipping 1,000 species list Ralph Peters shipment centers Europe ZFMK America Rutgers preservation in RNAlater Asia, AUS BGI Shenzhen
13 Sequencing and Assembly total RNA and mrna extraction cdna library construction illumina HiSeq 2000 ~ 2.5 GB raw data / species GB raw data assembly: SOAPdenovo-Trans sequence submission to Genbank
14 Data Exchange Data exchange and other FTPs Gerald Timelthaler
15 Sequence Submission SRA TSA
16 Sequence Submission Sequence Submission Standard practice Genbank, NCBI: restrictions not compatible with state-of-theart Next Generation Sequencing (NGS) data could not be applied to 1KITE data way to go: collaboration with NCBI Alex Donath
17 Sequence Submission Sequence Read Archive (SRA): Raw Data New possibilities because of 1KITE xml files with all necessary meta-data (collection details, experimental settings...) created from 1KITE database: faster, almost no manual interaction raw data upload via special proposal: aspera: ~250 GB on 1h 27 min (50 MB/s)
18 Sequence Submission Transcriptome Shotgun Archive (TSA): Assemblies Scaffolds not allowed neglects state-of-theart de novo transcriptome assemblers New possibilities because of 1KITE differentiation between ambiguous sequences and scaffolding possible 1KITE Umbrella Project
19 Tools for Analyses Software Tools for Analyses Orthograph (ZMB Bonn) PartitionFinder (ANU Canberra, ZMB Bonn) Aliscore, mare (ZMB Bonn) Alistat, Symtest (CES Canberra, ZMB Bonn) ExaML (HITS, Heidelberg) available on github or URLs
20 1KITE Database
21 1KITE Database Taxa Specimen (Inventory) Field Data (Locations) Sequences SUBPROJECTS User (Collaborators, Resposibilities)
22 1KITE Taxa Editor 1KITE Database
23 1KITE Locations Editor 1KITE Database
24 1KITE Inventory Editor 1KITE Database
25 1KITE Database: Prospects in progress: Sequences: several assemblies (datasets?) must be linked to each species implement search tool for taxa including sequences plus download (login and licence required) Subprojects: finish input mask fill in data for all species ; release for public build work-arounds for analysed datasets, or link to other databases (e.g., MorphDeBase)
26
27 1KITE Data Access 1KITE Species List
28 WIKI for 1KITE Members 1KITE WIKI newsletters progress reports collecting lists analyses tools up- / download possibilities discussion forum subproject pages -system
29 The 1KITE Consortium
30 Thanks to Barbara Holland and all organisers of this workshop and Thank you! Foto: Cowen Thanks to the 1KITE Consortium and David Yeates, Australian National Insect Collection, CSIRO Ecosystem Sciences, Canberra, Australia
31 Thanks to Barbara Holland and all organisers of this workshop and Thank you! Photo: A. Wild Thanks to the 1KITE Consortium and David Yeates, Australian National Insect Collection, CSIRO Ecosystem Sciences, Canberra, Australia
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