lecture_notes:04-05-2010
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lecture_notes:04-05-2010 [2010/04/05 22:10] hyjkim |
lecture_notes:04-05-2010 [2010/04/16 01:16] (current) karplus fixed citations to use Refnotes syntax |
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| Please add to or modify this page as you see fit! | Please add to or modify this page as you see fit! | ||
| + | =====Homework===== | ||
| + | Pick two or three assemblers. | ||
| + | * Find out where to get them | ||
| + | * How to install them | ||
| + | * What papers there are about them | ||
| + | * Create the wiki page about them | ||
| + | * And possibly install them | ||
| + | Volunteers: | ||
| + | * Phrap: Galt and Shyamini | ||
| + | * Velvet: Hyunsung and Galt | ||
| + | * ABySS: Galt and Chris | ||
| + | * AMOS: Shyamini and Herbert | ||
| + | * Arachne: John and Michael | ||
| + | * CAP3/PCAT: Michael and Galt | ||
| + | * Celera: Shyamini and Hyunsung | ||
| + | * Euler/Euler-sr: Herbert and John | ||
| + | * MIRA1: Herbert and Michael | ||
| + | * TIGR Assembler: John and Shyamini | ||
| + | * SHARCGS: Michael and Chris | ||
| + | * SSAKE: Herbert and Hyunsung | ||
| + | * Staden gap4 package: Michael and Hyunsung | ||
| + | * VCAKE: Chris and John | ||
| + | * Phusion: Shyamini and Michael | ||
| + | * QSRA: Herbert and Chris | ||
| + | * SOLiD System Tools (Corona_lite, etc): Hyunsung and Chris | ||
| + | * Newbler documentation: Galt and Herbert | ||
| + | * SOAPdenovo: Galt and Jenny | ||
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| + | Assembly Review Articles: | ||
| + | * Jason R. Miller, Sergey Koren and Granger Suttona [(cite:Miller2010>Jason R. Miller, Sergey Koren, Granger Sutton, Assembly algorithms for next-generation sequencing data, Genomics, In Press, Corrected Proof, Available online 6 March 2010, ISSN 0888-7543, DOI: 10.1016/j.ygeno.2010.03.001 http://www.sciencedirect.com/science/article/B6WG1-4YJ6GD8-1/2/ae6c957910e4ea658cdebff4a0ce9793)] \\ Covers these assemblers: SSAKE, SHARCGS, VCAKE, Newbler, Celera, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo.Compares de Bruijn graph to overlap/layout/consensus. | ||
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| =====Assembly Overview===== | =====Assembly Overview===== | ||
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| * Expect half your reads to have an error in them. | * Expect half your reads to have an error in them. | ||
| * Contiguous chromosomes with a low error rate ( output from assemblers). | * Contiguous chromosomes with a low error rate ( output from assemblers). | ||
| - | * Miami standard for a finished genome should have an error rate of 1 x 10^-5 bases. | + | * Bermuda standard for a finished genome should have an error rate of 1 x 10^-5 bases.1) [(cite:Bermuda1>[[http://www.genome.gov/page.cfm?pageID=10506376]])] [(cite:Bermuda2>[[http://www.ornl.gov/sci/techresources/Human_Genome/research/bermuda.shtml]])] |
| * To reduce error rate in short reads, stack up many reads and take the most common base at each position. | * To reduce error rate in short reads, stack up many reads and take the most common base at each position. | ||
| * How much data do we have? | * How much data do we have? | ||
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| - Can find repeat regions using paired-end data. | - Can find repeat regions using paired-end data. | ||
| * Most resquencing projects map reads to scaffolds and create contigs based upon mapping. Sections with missing read data can be assumed to be a deleting or an alteration to the existing scaffold. | * Most resquencing projects map reads to scaffolds and create contigs based upon mapping. Sections with missing read data can be assumed to be a deleting or an alteration to the existing scaffold. | ||
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| + | ===== References ===== | ||
| + | <refnotes>notes-separator: none</refnotes> | ||
| + | ~~REFNOTES cite~~ | ||
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lecture_notes/04-05-2010.1270505431.txt.gz ยท Last modified: 2010/04/05 22:10 by hyjkim
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