archive:computer_resources:assemblies
Differences
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| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
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archive:computer_resources:assemblies [2010/06/06 22:16] galt adding Ray, ABySS, and PCAP on Pog from README |
archive:computer_resources:assemblies [2010/06/12 02:14] mpcusack |
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| * euler-sr-assembly1/ | * euler-sr-assembly1/ | ||
| * mira | * mira | ||
| - | * mira-assembly1/ | + | * [[computer_resources:assemblies:mira:pog:mira-assembly1|]] |
| + | * [[computer_resources:assemblies:mira:pog:mira-assembly2|]] | ||
| * velvet | * velvet | ||
| * velvet-assembly1/ Assembling Pog 454 long reads with velvet. After very poor results with default settings, eventually started to get good results by getting the expected coverage (60) and cutoff (13) correct. It took a long time try different parameter settings. Also using the long reads as both short and long reads gave substantially better results. Because these were long reads, we could set k up to 31. Also tried with specially compiled version of velvet that could use k > 31, but can not report any improvement yet. Given that the average read is 370b, it should have been able to support longer k-values. Best results so far:\\ | * velvet-assembly1/ Assembling Pog 454 long reads with velvet. After very poor results with default settings, eventually started to get good results by getting the expected coverage (60) and cutoff (13) correct. It took a long time try different parameter settings. Also using the long reads as both short and long reads gave substantially better results. Because these were long reads, we could set k up to 31. Also tried with specially compiled version of velvet that could use k > 31, but can not report any improvement yet. Given that the average read is 370b, it should have been able to support longer k-values. Best results so far:\\ | ||
| Line 69: | Line 70: | ||
| N count: mean 0.0 sd 0.2 | N count: mean 0.0 sd 0.2 | ||
| U count: mean 11443.6 sd 65849.3 | U count: mean 11443.6 sd 65849.3 | ||
| - | Using Kevin's makefile, the blat alignments showed large contigs that looked basically correct. | + | Using Kevin's makefile, the blat alignments showed large contigs that looked basically correct, except for contig 8. |
| However many of them overlapped, unlike the Newbler output. This may have been due to a | However many of them overlapped, unlike the Newbler output. This may have been due to a | ||
| difference in the way Newbler and PCAP tried to handle the mixed population in the sample where | difference in the way Newbler and PCAP tried to handle the mixed population in the sample where | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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