trieste summer school – july 2011 cribi -...

Trieste Summer School – July 2011 CRIBI - Università di Padova


Mate pair signatures


Mate pair libraries


CRIBI APPROACH

STEP 1Use of insert length statistics for the identification of structural variations

STEP 2Use of sequence alignment (“splice-like” alignment) for the identification of the precise points of insertion/deletion.


FIRST STEP

• 4 indexes are created:

– unique MP, right distance, right orientation → useful for short indels(difference between observed and expected, after filtering low coverage)

– unique MP, wrong distance, rigth orientation → useful for long deletions(physical coverage)

– unique MP, wrong orientation → useful for inversions (physical coverage)

– unique reads lacking the partner → useful for long insertions (number of reads)


SECOND STEP

– The alignment of a structural variation aligns like a splicing site

– Reads that cover a breakpoint can be spliced-aligned, showing a pattern of alignment compatible with that specific structural variation

– By analysing these patterns, it is possibile to detect the correct breakpoint with a base-precision


FIRST STEP: LONG-DELETIONS AND INVERSIONS


Long deletions


Short deletions


FIRST STEP: LONG INSERTIONS


Long insertions


Inversions and more


• random genome

• structural variations randomly added (type, position, length, hetero/homozygosity)

• SNP random added (type, position, nucleotide)

SV \ Coverage 5X 10X 20X 40X

DELETIONS 58% 59% 72% 90%

INSERTIONS 43% 76% 78% 85%

INVERSIONS 56% 58% 74% 88%

Results on random SV

trieste summer school – july 2011 cribi -...

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