AMOS Assembly Validation and Visualization

42 Pages·2006·2.33 MB·English

by  Michael Schatz

AMOS Assembly Validation
and Visualization
Michael Schatz
Center for Bioinformatics and Computational Biology
University of Maryland
April 7, 2006
Outline
AMOS Introduction
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Getting Data into AMOS
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AMOS Validation Pipeline
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Mate-Based Validation
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C/E Statistic
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Read Alignment Validation
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Read Depth Validation
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AMOS Assembly Investigator
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Contigs, Inserts, Histograms, SNP Barcode, Features
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Misassembly Walkthrough
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Demo
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Outline
AMOS Introduction Slides available at:
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Getting Data into AMOS
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http://www.cbcb.umd.edu/~mschatz/
AMOS Validation Pipeline
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Mate-Based Validation
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C/E Statistic
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Read Alignment Validation
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Read Depth Validation
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AMOS Assembly Investigator
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Contigs, Inserts, Histograms, SNP Barcode, Features
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Misassembly Walkthrough
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Demo
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AMOS Goals
Open Source Assembly Package
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http://amos.sourceforge.net
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Modular design
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Flexibility in building “pipelines”
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Well defined input/output formats
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General use: does not depend on databases,
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proprietary data formats, specialized hardware,
etc.
Modular Design
scaffolder
overlapper
Bank
reads
error A A viewer
inserts
P P
corrector
I overlaps I
contigs ...
scaffolds
etc.
contigger
etc.
Converters: Celera Assembler, .ACE, TIGR Assembler, Trace Archive
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Overlapper
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Contigger (Minimus)
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Consensus caller
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Comparative assembler (AMOScmp)
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Mate-pair based QC tool
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Viewer (Assembly Investigator)
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Pipeline executor
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Assembly Data Conversions
.seq
bank2fasta
.qual
.fasta
AMOS
.mates bank-transact
toAmos bank2contig
Message
AMOS
.asm
.contig
File
Bank
bank-report
.frg bank2scaff
.afg
.contig .bnk/ .scaffolds.fasta
.ace
CA Assembly w/ Surrogates to AMOS Message File (.asm, .frg)
$ toAmos –a prefix.asm –f prefix.frg –o prefix.afg –S
Finished Assembly to AMOS Message File (.contig, .frg)
$ toAmos –f prefix.frg –c prefix.contig –o prefix.afg
AMOS Message File to Bank
$ bank-transact –m prefix.afg –b prefix.bnk -c
AMOS Validation Pipeline
Automatically scan an assembly to locate
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misassembly signatures for further analysis
and correction
cavalidate prefix (.frg, .asm)
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Load CA Assembly Data into Bank
1.
Evaluate Mate Pairs & Libraries
2.
Evaluate Read Alignments
3.
AMOS
Analyze Depth of Coverage
4. Bank
List Surrogates
5.
Load Misassembly Signatures into Bank
6.
amosvalidate prefix (.afg)
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Same as cavalidate, except skips surrogates
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Mate-Happiness: asmQC
Evaluate mate “happiness” across assembly
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Happy = Correct orientation and distance
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Finds regions with multiple:
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Compressed Mates
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Expanded Mates
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Invalid same orientation ((cid:198) (cid:198))
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Invalid outie orientation ((cid:197) (cid:198))
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Missing Mates
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Linking mates (mate in a different scaffold)
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Singleton mates (mate is not in any contig)
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Regions with high C/E statistic
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Mate-Happiness: asmQC
Excision: Skip reads between flanking repeats
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Truth
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Misassembly: Compressed Mates, Missing Mates
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Mate-Happiness: asmQC
Insertion: Additional reads between flanking repeats
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Truth
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Misassembly: Expanded Mates, Missing Mates
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