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lecture-23-handouts - Practical Bioinformatics for Life...

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11/7/2011 1 Practical Bioinformatics for Life Scientists Week 12, Lecture 23 István Albert Bioinformatics Consulting Center Penn State Genome Assembly From sequencing reads to whole genomes Multistep process 1. Assemble short reads into longer sequences contigs 2. Scaffolding arrange contigs relative to one another or as seen on a similar known genome 3. Genome finishing (gap closure) fill in gaps with directed sequencing procedures and manual curation AMOS A Modular Open-Source whole genome assembler It is not a single software rather than a collection of interoperable tools, standards and techniques Read assembly challenges repeated elements: RPT A1 and RPT A2 A valid assembly of two contigs instead of one Images and content from http://www.cbcb.umd.edu/research/assembly_primer.shtml Other challenges: genomic variation, heterozygosity, copy number variation misassembly due to sequencing errors chimeric
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11/7/2011 2 Scaffolding Orienting contigs via paired end (or mate-pair)
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