A year of happy MAPping

May Jun Aug

Sep

July

Oct Nov Dec

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Nick Loman

Breakfast meetingMinION is unique:• Real-time• Portable• Super long reads

A year of happy MAPping

May Jun Aug

Sep

July

Oct Nov Dec

Jan Feb AprMar

Nick Loman

Lambda burn-in

Do you remember your first read?

10.6084/m9.figshare.1052996

One diagnostic read

poretools

May Jun Aug

Sep

July

Oct Nov Dec

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Outbreak

May Jun Aug

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July

Oct Nov Dec

Jan Feb AprMar

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

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

gigasciencejournal.com/content/3/1/22/

Nanocorrect

biorxiv.org/content/early/2015/03/11/015552

E. coli single contig assembly

biorxiv.org/content/early/2015/03/11/015552

Ebola

May Jun Aug

Sep

July

Oct Nov Dec

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http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3290.html

www.nature.com/nmeth/journal/v12/n4/full/nmeth.3327.html

http://www.nature.com/news/data-sharing-make-outbreak-research-open-access-1.16966

Dstl Protocol Development• Two approaches tried on archived Ebola RNA:– Genome tiling amplicon: RT-PCR– Direct metagenomics: Ebola-spiked sample

• Validation with MiSeq

3khz / MAP-004 update

Portability

May Jun Aug

Sep

July

Oct Nov Dec

Jan Feb AprMar

So, what happened in April?

May Jun Aug

Sep

July

Oct Nov Dec

Jan Feb AprMar

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

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