1. SSAHA_pileup:
A Genome Variation Detection Pipeline for
Various Sequencing Platforms
Photo Credit: saynine on flickr.com
Ben Blackburne
Wellcome Trust Sanger Institute
3. Introduction
●New sequencing technologies
– More data
– Different kinds of data
●Solexa, 454
●capillary, too
– Diploid genomes
– SNPs, indels, VNTRs
Photo Credit: mknowles on flickr.com
4.
5.
6.
7. SSAHA_pileup
●Sequence Search and Alignment by Hashing
Algorithm
●SSAHA_SNP
– Global positioning with SSAHA algorithm
– Fast Smith-Waterman implementation (from
Cross_Match)
– Identification of best match
●SSAHA_pileup
– Determines SNPs from set of best alignments
●Works on Solexa, 454, and capillary reads
12. SSAHA_SNP
chr n
score: 126
Local Mapping
(Smith-Waterman)
score: 113
chr m
13. SSAHA_SNP
chr n
score: 126
Select best match
score: 113
chr m
14. SSAHA_SNP
●Read pair information
– currently possible with
extra step using SSAHA2
– being integrated into
SSAHA_SNP
– Removes incorrectly
mapped pairs
Photo Credit: Matthew Fang on flickr.com
28. Filtering
●Processes that cause bogus SNPs
– Incorrect global mapping
– Incorrect local alignment
– Poor quality reads
– Sequence amplification errors
29. Global Mapping Problems
●Reads from unmapped regions of the genome
– Lead to absurdly high apparent coverage
chr n
` ` `
` ` `
`
` `` ` ` ``
`
chr m
30. Global Mapping Problems
●Reads from unmapped regions of the genome
– Lead to absurdly high apparent coverage
chr n
` ` `
` ` `
`
` `` ` ` ``
`
chr m
31. Global Mapping Problems
●Reads from unmapped regions of the genome
– Lead to absurdly high apparent coverage
chr n
`
`
` ``
`
`
`
`
`
` `
``
`
45. Conclusions
●SSAHA_pileup is effective across both new and
old sequencing technologies
●Questions
– When is a SNP not a SNP?
– Homozygous/Heterozygous SNPs
46. Conclusions
●SSAHA_pileup is effective across both new and
old sequencing technologies
●Questions
– When is a SNP not a SNP?
– Homozygous/Heterozygous SNPs
●Length matters...?
– But it's what you do with it that counts
47. Obtaining SSAHA_pileup
SSAHA_pileup:
ftp://ftp.sanger.ac.uk/pub/zn1/ssaha_pileup/
SSAHA2:
http://www.sanger.ac.uk/Software/analysis/SSAHA2/
These Slides:
http://slideshare.net/bpb/
