Alignment methods. Martijn Vermaat Department of Human Genetics Center for Human and Clinical Genetics
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1 Alignment methods Martijn Vermaat Department of Human Genetics Center for Human and Clinical Genetics
2 Alignment methods Sequence alignment Assembly vs alignment Alignment methods Common issues Platform specifics Software Metagenomics course 1/28 Thursday, 7 February 2013
3 Sequence alignment Identifying regions of similarity in sequences Metagenomics course 2/28 Thursday, 7 February 2013
4 Sequence alignment Identifying regions of similarity in sequences In NGS Recovering original nucleotide sequence... from many short fragments... using a known reference Metagenomics course 2/28 Thursday, 7 February 2013
5 Sequence alignment Pairwise alignment Metagenomics course 3/28 Thursday, 7 February 2013
6 Sequence alignment Multiple sequence alignment Metagenomics course 4/28 Thursday, 7 February 2013
7 Sequence alignment Global vs local alignment Metagenomics course 5/28 Thursday, 7 February 2013
8 Sequence alignment Structural alignment Metagenomics course 6/28 Thursday, 7 February 2013
9 Assembly vs alignment Alignment methods Sequence alignment Assembly vs alignment Alignment methods Common issues Platform specifics Software Metagenomics course 7/28 Thursday, 7 February 2013
10 Assembly vs alignment Assembly Metagenomics course 8/28 Thursday, 7 February 2013
11 Assembly vs alignment Assembly Alignment Metagenomics course 8/28 Thursday, 7 February 2013
12 Assembly vs alignment Assembly Memory hungry Needs high coverage Metagenomics course 9/28 Thursday, 7 February 2013
13 Assembly vs alignment Assembly Memory hungry Needs high coverage Alignment Easy to do in parallel Restricted by reference sequence highly polymorphic regions large insertions Metagenomics course 9/28 Thursday, 7 February 2013
14 Alignment methods Alignment methods Sequence alignment Assembly vs alignment Alignment methods Common issues Platform specifics Software Metagenomics course 10/28 Thursday, 7 February 2013
15 Alignment methods Smith-Waterman Generalization of Needleman-Wunsch Guaranteed optimal alignment A C A C A C T A A G C A C A C A gap penalty = 1 match=+2 mismatch= 1 Metagenomics course 11/28 Thursday, 7 February 2013
16 Alignment methods 2-step alignment Metagenomics course 12/28 Thursday, 7 February 2013
17 Alignment methods 2-step alignment Step 1: Find candidate positions Use read seeds Hash table-based or Burrows-Wheeler transform-based heuristic Balance between speed and accuracy Metagenomics course 12/28 Thursday, 7 February 2013
18 Alignment methods 2-step alignment Step 2: Align and report Complete alignment with Smith-Waterman Evaluate alignment(s) Metagenomics course 12/28 Thursday, 7 February 2013
19 Common issues Alignment methods Sequence alignment Assembly vs alignment Alignment methods Common issues Platform specifics Software Metagenomics course 13/28 Thursday, 7 February 2013
20 Common issues Insertions and deletions (indels) Metagenomics course 14/28 Thursday, 7 February 2013
21 Common issues Insertions and deletions (indels) Local realignment around indels Per-Base Alignment Qualities (BAQ) Metagenomics course 14/28 Thursday, 7 February 2013
22 Common issues Non-unique alignment How to report non-unique alignments? Metagenomics course 15/28 Thursday, 7 February 2013
23 Common issues Non-unique alignment How to report non-unique alignments? Discard entirely Choose one randomly Report all with best quality above some quality Depends on the tool Metagenomics course 15/28 Thursday, 7 February 2013
24 Common issues Structural variation Chromosomal relocation Inversion Large indels Copy-number variation Use specialized tools Metagenomics course 16/28 Thursday, 7 February 2013
25 Common issues Split-read mapping Allow aligned read to be split For example RNA reads on DNA reference Metagenomics course 17/28 Thursday, 7 February 2013
26 Common issues Split-read mapping Allow aligned read to be split For example RNA reads on DNA reference Metagenomics course 17/28 Thursday, 7 February 2013
27 Common issues Circular alignment Circular genome (e.g. bacteria, mitochondria) Metagenomics course 18/28 Thursday, 7 February 2013
28 Common issues Circular alignment Circular genome (e.g. bacteria, mitochondria) Most aligners assume linear reference Metagenomics course 18/28 Thursday, 7 February 2013
29 Common issues Circular alignment Circular genome (e.g. bacteria, mitochondria) Most aligners assume linear reference Trick: extend reference Metagenomics course 18/28 Thursday, 7 February 2013
30 Common issues Circular alignment Circular genome (e.g. bacteria, mitochondria) Most aligners assume linear reference Trick: extend reference copy first N bases to the end Metagenomics course 18/28 Thursday, 7 February 2013
31 Common issues Circular alignment Circular genome (e.g. bacteria, mitochondria) Most aligners assume linear reference Trick: extend reference copy first N bases to the end restore alignment to original reference Metagenomics course 18/28 Thursday, 7 February 2013
32 Platform specifics Alignment methods Sequence alignment Assembly vs alignment Alignment methods Common issues Platform specifics Software Metagenomics course 19/28 Thursday, 7 February 2013
33 Platform specifics Paired-end sequencing Metagenomics course 20/28 Thursday, 7 February 2013
34 Platform specifics Paired-end sequencing Align reads separately Choose from non-unique alignments based on pairing Metagenomics course 20/28 Thursday, 7 February 2013
35 Platform specifics Color-space (or SOLiD) reads Used by 454, Solexa, SOLiD systems Di-nucleotide encoding Needs support from alignment software Metagenomics course 21/28 Thursday, 7 February 2013
36 Platform specifics Color-space (or SOLiD) reads Used by 454, Solexa, SOLiD systems Di-nucleotide encoding Needs support from alignment software Metagenomics course 21/28 Thursday, 7 February 2013
37 Platform specifics Color-space (or SOLiD) reads Decoding Metagenomics course 22/28 Thursday, 7 February 2013
38 Error profile Platform specifics Homopolymers CG-content Positional (example shown) Metagenomics course 23/28 Thursday, 7 February 2013
39 Software Alignment methods Sequence alignment Assembly vs alignment Alignment methods Common issues Platform specifics Software Metagenomics course 24/28 Thursday, 7 February 2013
40 Software Some popular aligners for NGS Hash table-based Eland MAQ Metagenomics course 25/28 Thursday, 7 February 2013
41 Software Some popular aligners for NGS Hash table-based Eland MAQ Burrows-Wheeler Transform-based Bowtie BWA Metagenomics course 25/28 Thursday, 7 February 2013
42 Software Some popular aligners for NGS Hash table-based Eland MAQ Burrows-Wheeler Transform-based Bowtie BWA Split-read alignment Tophat GSNAP Mosaik Metagenomics course 25/28 Thursday, 7 February 2013
43 Viewers Software IGV, Savant, Geneyous, Tablet Metagenomics course 26/28 Thursday, 7 February 2013
44 Viewers Software IGV, Savant, Geneyous, Tablet tview (console-based) Metagenomics course 26/28 Thursday, 7 February 2013
45 Viewers Software IGV, Savant, Geneyous, Tablet tview (console-based) UCSC Genome Browser, GBrowse (web-based) Metagenomics course 26/28 Thursday, 7 February 2013
46 Questions? Acknowledgements: Jeroen Laros Bas E. Dutilh Metagenomics course 27/28 Thursday, 7 February 2013
47 Questions? Image sources cbsu.tc.cornell.edu/ngw2010/day2 lecture1.pdf en.wikipedia.org/wiki/sequence alignment en.wikipedia.org/wiki/multiple sequence alignment mcs2/teaching/biocomp/tutorials/global.html -throughput-sequencing-data.php biotechnology biology chemistry/biotechnology/genes genetic engineering/genes nature concept and synthesis/biotech physical nature dna.php omega.rc.unesp.br/mauricio/curso/bibliografia/22/362/dibase%20sequencing%20and%20color%20space %20Analysis.pdf cgrlucb.wikispaces.com/samtoolsspring2012 and some of my own Metagenomics course 28/28 Thursday, 7 February 2013
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