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

Info iconThis preview shows pages 1–6. Sign up to view the full content.

View Full Document Right Arrow Icon
Practical Bioinformatics for Life Scientists Week 12, Lecture 23 István Albert Bioinformatics Consulting Center Penn State
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
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
Background image of page 2
AMOS A Modular Open-Source whole genome assembler It is not a single software rather than a collection of interoperable tools, standards and techniques
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
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
Background image of page 4
Scaffolding Orienting contigs via paired end (or mate-pair) information
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 6
This is the end of the preview. Sign up to access the rest of the document.

Page1 / 16

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

This preview shows document pages 1 - 6. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online