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The Genome Assemblies of Tasmanian Devil. Zemin Ning The Wellcome Trust Sanger Institute. Outline of the Talk:. The Phusion2 pipeline Flow-sorting sequencing Assigning contigs to individual chromosomes The Devil genome assembly Future work. Phusion2 Assembly Pipeline. Assembly.

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The Genome Assemblies of Tasmanian Devil

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The genome assemblies of tasmanian devil

The Genome Assemblies of

Tasmanian Devil

Zemin Ning

The Wellcome Trust Sanger Institute


The genome assemblies of tasmanian devil

Outline of the Talk:

  • The Phusion2 pipeline

  • Flow-sorting sequencing

  • Assigning contigs to individual chromosomes

  • The Devil genome assembly

  • Future work


The genome assemblies of tasmanian devil

Phusion2 Assembly Pipeline

Assembly

Data Process

Solexa

Reads

Supercontig

Long Insert Reads

PRono

Fuzzypath

Contigs

Reads Group

2x75 or 2x100

Base

Correction

Velvet

Phrap

GraphRP


The genome assemblies of tasmanian devil

Mis-assembly Errors: Contig Break based on Inconsistent Pairs


The genome assemblies of tasmanian devil

Mis-assembly Errors:

Contig Break Based on Pair Coverage


The genome assemblies of tasmanian devil

Pipeline of Contig Gap Closure


The genome assemblies of tasmanian devil

Sequencing T. Devil on Illumina: Strategy

Tumour or normal genomic DNA

Fragments of defined size

0.5, 2, 5, 7, 8, 10 kb

Sequencing

2x100bp reads short insert

2x50bp mate pairs

Sequencing performed at Illumina

Alignment using bwa, smalt

De novo Assembly

Somatic mutations

Germline variants


The genome assemblies of tasmanian devil

Table 1 Run ID, Template names, Number of reads and Chromosome size

4972_1 chr1 IL20_4972:1 19.8 571

4967_1 chr2 IL21_4967:1 20.0 610

4971_1 chr3 IL30_4971:1 21.7 556

4964_1 chr4 IL14_4964:1 7.26 450

4969_1 chr5 IL17_4969:1 7.06 341

4969_2 chr6 IL17_4969:2 8.59 277

4969_3 chrx IL17_4969:3 9.43 122

Read mapping coefficient:

e = Size_of_Chr/Num_reads_in_lane


The genome assemblies of tasmanian devil

New Data Sequenced by Illumina

Chr1EAS25_101_170549

Chr1EAS25_101_270549

Chr2EAS25_101_370580

Chr2EAS25_101_470580

Chr3EAS25_101_570547

Chr3EAS25_101_670547

Chr4EAS188_173_370448

Chr4EAS188_173_470448

Chr5EAS188_173_570346

Chr5EAS188_173_670346

Chr6EAS188_173_770285

Chr6EAS188_173_870285

ChrxEAS188_173_270122


The genome assemblies of tasmanian devil

Table 2 Chr_ID, Chr_size, Contigs_assigned Bases_assigned N_reads

Chr1 571 65262604 19.8

Chr2 610 76959 673 20.0

Chr3 556 68842 58521.7

Chr4 450 48352 4467.26

Chr5 341 30451 279 7.06

Chr6 277 25726 2508.59

Chrx 122 14189 83.69.53

Unassigned 6084154.7 (1.8%)


The genome assemblies of tasmanian devil

New Data Sequenced by Illumina

Table 2 Chr_ID, Chr_size, Contigs_assigned Bases_assigned Mb

Chr1 571 6729684

Chr2 610 8381 740

Chr3 556 7197 641

Chr4 450 4817 487

Chr5 341 3188 300

Chr6 277 2844 263

Chrx 122 2378 86.6

Unassigned 440 1.23


The genome assemblies of tasmanian devil

Unassigned contigs were placed by supercontigs using mate pairs


The genome assemblies of tasmanian devil

Genome Assembly Normal – T. Devil

Solexa reads:

Number of read pairs: 650 Million;Finished genome size: 3.3 GB;

Read length:2x100bp;

Estimated read coverage: ~40X;

Insert size: 410/50-600 bp;

Mate pair data:2k,4k,5k,6k,8k,10k

Number of reads clustered:591 Million

Assembly features: - stats

Contigs SupercontigsTotal number of contigs: 237,29135,974

Total bases of contigs: 2.93 Gb3.17 Gb

N50 contig size: 20,1391,847,186

Largest contig:189,8665,315,556

Averaged contig size: 12,35488,254

Contig coverage on genome: ~94%>99%

Ratio of placed PE reads:~92%?


The genome assemblies of tasmanian devil

Acknowledgements:

  • Elizabeth Murchuson

  • David McBride

  • Fengtang Yang

  • Mike Stratton

  • Ole Schulz-Trieglaff

  • Dirk Evers

  • David Bentley


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