quality of assemblies mouse
Download
Skip this Video
Download Presentation
Quality of assemblies—mouse

Loading in 2 Seconds...

play fullscreen
1 / 29

Quality of assemblies mouse - PowerPoint PPT Presentation


  • 61 Views
  • Uploaded on

Quality of assemblies—mouse. Terminology: N50 contig length If we sort contigs from largest to smallest, and start Covering the genome in that order, N50 is the length Of the contig that just covers the 50 th percentile. 7.7X sequence coverage. Quality of assemblies—dog. 7.5X

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Quality of assemblies mouse' - iman


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
quality of assemblies mouse
Quality of assemblies—mouse

Terminology:N50 contig length

If we sort contigs from largest to smallest, and start

Covering the genome in that order, N50 is the length

Of the contig that just covers the 50th percentile.

7.7X

sequence

coverage

quality of assemblies dog
Quality of assemblies—dog

7.5X

sequence

coverage

quality of assemblies chimp
Quality of assemblies—chimp

3.6X

sequence

Coverage

Assisted

Assembly

history of wga
History of WGA

1997

  • 1982: -virus, 48,502 bp
  • 1995: h-influenzae, 1 Mbp
  • 2000: fly, 100 Mbp
  • 2001 – present
    • human (3Gbp), mouse (2.5Gbp), rat*, chicken, dog, chimpanzee, several fungal genomes

Let’s sequence the human genome with the shotgun strategy

That is impossible, and a bad idea anyway

Phil Green

Gene Myers

slide5

$985 deCODEme

(November 2007)

$399 Personal Genome Service

(November 2007)

$2,500 Health Compass service

(April 2008)

Genetic Information Nondiscrimination Act

(May 2008)

$350,000 Whole-genome sequencing

(November 2007)

slide6

Applications

Whole-genome sequencing

Comparative genomics

Genome resequencing

Structural variation analysis

Polymorphism discovery

Metagenomics

Environmental sequencing

Gene expression profiling

Genotyping

Population genetics

Migration studies

Ancestry inference

Relationship inference

Genetic screening

Drug targeting

Forensics

slide7

New sequencing applications

Sequencing applications

Increase in sequencing data output

Demand for more sequencing

Sequencing technology improvement

slide8

Sequencing technology

Sanger sequencing

$10.00

$1.00

Cost per finished bp:

$0.10

$0.01

1975

1980

1990

2000

2008

Fred Sanger

Read length:

15 – 200 bp

500 – 1,000 bp

Throughput:

“grad-student years”

2 ∙ 106 bp/day

slide9

Sequencing technology

Sanger sequencing

3 ∙ 109 bp

1x coverage

10x coverage

× 3 ∙ 109 bp

= 40 years

2 ∙ 106 bp/day

= $30 million

10x coverage × 3 ∙ 109 bp × $0.001/bp

pyrosequencing on a chip
Pyrosequencing on a chip
  • Mostafa Ronaghi, Stanford Genome Technologies Center
  • 454 Life Sciences
slide11

Sequencing technology

Next-generation sequencing

“short reads”

Read length:

250 bp

Throughput:

300 Mb/day

Cost:

~ 10,000 bp/$

De novo:

yes

Genome Sequencer / FLX

slide13

Sequencing technology

Next-generation sequencing

Genome Analyzer

SOLiD Analyzer

“microreads”

Read length:

~ 35 bp

Throughput:

300 – 500 Mb/day

Cost:

~ 100,000 bp/$

De novo:

yes

slide14

Sequencing technology

Next-generation sequencing

Genome Analyzer

SOLiD Analyzer

reads

Read length:

~ 50-150 bp

Throughput:

3 Gb/day

Cost:

~ 3,000,000 bp/$

De novo:

yes

complete genomics
Complete Genomics
  • $5,000 this summer
    • Quality?...
  • 1,000 genomes in 2009
  • 20,000 genomes in 2010
so how fast is cost going down
So, how fast is cost going down?
  • 2006: $10 million
  • 2008: $100,000
  • 2009: $10,000
  • ? $1,000
  • ??? $100
slide21

Sequencing technology

Next-generation sequencing

“SNP chips”

Infinium Assay

GeneChip Array

genotypes

Read length:

1bp

Throughput:

1 – 2 Mb/day

Cost:

5,000 bp/$

De novo:

no

nanopore sequencing
Nanopore Sequencing

http://www.mcb.harvard.edu/branton/index.htm

slide23

Sequencing technology

Next-generation sequencing

evolution at the dna level
Evolution at the DNA level

Deletion

Mutation

…ACGGTGCAGTTACCA…

SEQUENCE EDITS

…AC----CAGTCCACCA…

REARRANGEMENTS

Inversion

Translocation

Duplication

evolutionary rates
Evolutionary Rates

next generation

OK

OK

OK

X

X

Still OK?

ad