Analysis of NGS Data
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1 Analysis of NGS Data Introduction and Basics Folie: 1
2 Overview of Analysis Workflow Images Basecalling Sequences denovo - Sequencing Assembly Annotation Resequencing Alignments Comparison to reference (variation, read distribution, read frequencies) Folie: 3
3 Overview of Analysis Workflow Images Basecalling Primary Analysis (on sequencer using vendor`s software) Sequences denovo - Sequencing Assembly Annotation Resequencing Alignments Comparison to reference (variation, read distribution, read frequencies) Folie: 4
4 Overview of Analysis Workflow Images Basecalling Sequenzen denovo - Sequencing Assembly Annotation Resequencing Alignments Secondary Analysis (on downstream computers using open-source Tools or vendor`s software) Comparison to reference (variation, read distribution, read frequencies) Folie: 5
5 Overview of Analysis Workflow Images Basecalling Sequences denovo - Sequencing Assembly Annotation Resequencing Alignments Comparison to reference (variation, read distribution, read frequencies) Tertiary Analysis (on downstream computers Using open-source Tools or vendor`s software) Folie: 6
6 Overview of Data Amounts and Formats Several TB Images Basecalling Hundreds of GB Sequences denovo - Sequencing FASTA Assembly Annotation TXT-Formate FASTQ Resequencing Alignments SAM, BAM, TXT Comparison to reference (variation, read distribution, read frequencies) Hundreds of GB Few GB or less Folie: 7
7 Resequencing Genome of sequenced organism already known WGS: Sequencing of complete DNA Target-Enriched: Enrichment of specific target regions prior to sequencing Folie: 11
8 Alignment Identify the origin of each read in the original genome Difficulties: short reads (36 bp 400 bp) many reads (several millions) sequencing errors genomic variation Folie: 12
9 SAM / BAM Format SAM Format Specification (v1.4-r962) Alignment-Startposition (1-basiert) Folie: 21
10 SAM / BAM Format SAM Format Specification (v1.4-r962) Alignment Quality -10 log10 P(alignment position is wrong) in [0,255], 255 for not available Folie: 22
11 SAM / BAM Format SAM Format Specification (v1.4-r962) CIGAR String Folie: 23
12 SAM / BAM Format SAM Format Specification (v1.4-r962) reference name of next partner read = : same reference * : not available Folie: 24
13 SAM / BAM Format SAM Format Specification (v1.4-r962) Alignment position of next partner read Folie: 25
14 SAM / BAM Format SAM Format Specification (v1.4-r962) Fragmentsize 0: single read or not available Folie: 26
15 SAM / BAM Format SAM Format Specification (v1.4-r962) Sequence Folie: 27
16 SAM / BAM Format SAM Format Specification (v1.4-r962) Basecalling qualities for each base of read * : not available Folie: 28
17 SAM / BAM Format SAM Format Specification (v1.4-r962) Optional fields following the TAG:TYPE:VALUE format (here: edit-distance) Folie: 29
18 Folie: 30
19 Folie: 31
20 Folie: 32
21 Software Seed-and-Extend BWT-Based MAQ BWA Eland (Illumina) Bowtie BFAST SOAP2 Mosaik Differ in Stampy ability to do gapped alignment read length requirements NovoAlign ability to do PE-alignment speed and memory footprint Folie: 33
22 Variantcalling (SNPs/Indels) Bayesian Approach P( D g ) P( g ) P( g D) = P( D) Folie: 34
23 Variantcalling SNPs Pileup of reads against reference sequence Filter: - Basequality Alignmentquality Frequency of variant Variant in both forward and reverse reads Folie: 35
24 Variantcalling Indels Pileup of reads against reference sequence Generation of candidate haplotypes Realignment of reads against candidate haplotypes Probability of each candidate haplotype Folie: 36
25 Variantcalling Indels Dindel: Accurate indel calls from short-read data C.A. Albers et al. Genome Research 2011 Folie: 37
26 Variantcalling SVs Anomalous PE-alignment deletion in sample Folie: 38
27 Variantcalling SVs Anomalous PE-alignment insertion in sample Folie: 39
28 Variantcalling SVs Anomalous PE-alignment inversion in sample Folie: 40
29 Variantcalling SVs Anomalous PE-alignment Chr B Chr A inter-chromosomal rearrangement Folie: 41
30 Variantencalling SVs Partially aligning reads partially aligned reads completely aligned reads deletion Folie: 42
31 Software SNPs / Indels - Samtools (Sanger) - GATK (Broad) - SOAP (BGI) (SNPs only) - Vendor`s software Indels - Dindel (Sanger) SVs - BreakDancer - CREST Folie: 43
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