2014 10-01-assembly summaryvariantsoverview
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Transcript of 2014 10-01-assembly summaryvariantsoverview
Wednesday Mini Overview
Congrats!• first ever genome assembly
• complete approach
• with real-world cutting edge tools
• Some shortcuts:
• we used 2% of a eukaryotic (ant) genome
• only 1 type of paired reads
• only used “one-step” software.
So you want to do sequence a genome…
• Sampling? • algorithms prefer low diversity
• Sequencing approach? • paired end? • which sequencer? • what is needed for scaffolding?
Scaffolding
So you want to do sequence a genome…
• Sampling? • algorithms prefer low diversity
• Sequencing approach? • paired end? • which sequencer? • what is needed for scaffolding?
• input data Q/A? • sequencer statistics • fastqc • bio-relevant measurements? (e.g. % mapping to known data)
Unable to detect all errors!
• trimming/deduplicating/filtering • removing excess/redundant data • removing errors
• Which assembler? • used by others? (publications/ online list/ forum/
assemblathon) • something new? !
• assembly result QA • sequence statistics (e.g., QUAST) • bio-relevant measures (e.g. ,CEGMA)
So you want to do sequence a genome…
Perfect parameters
• Instead: need to test many combinations
• of trimming
• of filtering
• different assembly software
Take home messages• No “best way”
• Need to install a lot of software
• A lot of work in UNIX - to launch software, to convert formats…
• Need to test many parameters
• Be careful with qualities!
No need to understand everything!
20% effort for 80% result
Calling variants
www.sciencemag.org SCIENCE VOL 331 25 FEBRUARY 2011 1067
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Solenopsis invicta fire ants are a big problem!very well studied!
Ascunce et al 2011
Solenopsis invicta fire ant: two social forms
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•1 large queen •Independent founding •Highly territorial •Many sizes of workers
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•2-100 smaller queens •Dependent founding •No inter-colony aggression •All workers similar size
Single-queen form: Multiple-queen form: