AMOS Assembly Validation & Finishing

42 Pages·2017·2.29 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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