london calling: a year of happy mapping 14th may 2015
TRANSCRIPT
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A year of happy MAPping
May Jun Aug
Sep
July
Oct Nov Dec
Jan Feb AprMar
Nick Loman
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Breakfast meetingMinION is unique:• Real-time• Portable• Super long reads
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A year of happy MAPping
May Jun Aug
Sep
July
Oct Nov Dec
Jan Feb AprMar
Nick Loman
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Lambda burn-in
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Do you remember your first read?
10.6084/m9.figshare.1052996
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One diagnostic read
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poretools
May Jun Aug
Sep
July
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Outbreak
May Jun Aug
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July
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Species IDAlign MinION reads to taxa specific genes (MetaPhlA2) using LAST.
S.enterica identified in under 30 mins
Serogroup IDAlign minION reads to S.enterica reference genome. Phylogenetic placement with pplacer
Within 50 mins we could identify the strains as serotype Enteritidis
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Outbreak IDAlignment of MinION reads to Salmonella Enteritidis reference genome. Phylogenetic placement with pplacer
Within 100 minutes the outbreak strains was unambiguously part of the national 14b cluster (RED) and the sporadic cases (BLUE) was indeed sporadic
Quick et al – Genome Biology in press
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gigasciencejournal.com/content/3/1/22/
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Nanocorrect
biorxiv.org/content/early/2015/03/11/015552
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E. coli single contig assembly
biorxiv.org/content/early/2015/03/11/015552
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Ebola
May Jun Aug
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July
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Jan Feb AprMar
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http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3290.html
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www.nature.com/nmeth/journal/v12/n4/full/nmeth.3327.html
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http://www.nature.com/news/data-sharing-make-outbreak-research-open-access-1.16966
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Dstl Protocol Development• Two approaches tried on archived Ebola RNA:– Genome tiling amplicon: RT-PCR– Direct metagenomics: Ebola-spiked sample
• Validation with MiSeq
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3khz / MAP-004 update
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Portability
May Jun Aug
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So, what happened in April?
May Jun Aug
Sep
July
Oct Nov Dec
Jan Feb AprMar
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Wish ListWhat now?• Fast mode / more pores– Diagnostic & environmental
metagenomics• Rapid sample prep• (very) Low input• Direct RNA sequencing
MinION is unique:• Real-time • Portable• Super long reads
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AcknowledgementsOxford Nanopore• Clive Brown• Zoe Macdougall• Daniel Turner• Stephanie Brooking• Oliver Hartwell• Gordon Sanghera• Spike Willcocks• Roger Pettett• Stodders• Apollo Steve• Bhupinder• ..and the entire team
Dstl Porton Down• Simon Weller• Phil Rachwal• Jamie Taylor
Heartlands Hospital• Peter Hawkey
Public Health England• Phil Ashton• Tim Dallman
GigaScience• Scott Edmunds
University of Birmingham• Cathy Wardius• Szymon Calus
Josh Quick