archive:computer_resources:assemblies
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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 [2010/04/22 20:27] karplus added largest contig size for newbler-assembly1 |
archive:computer_resources:assemblies [2010/04/23 07:52] galt |
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| * mira-assembly1/ | * mira-assembly1/ | ||
| - | * velvet-assembly2/ 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:\\ |
| * Final graph has 1755 nodes and n50 of 41723, max {contig size} 142286, total {genome size} 2468925. | * Final graph has 1755 nodes and n50 of 41723, max {contig size} 142286, total {genome size} 2468925. | ||
| - | * velvet-assembly3/ Assembling Pog Solid mate-paired 26b reads with velvet in double-encoded colorspace. Not had time to optimize parameters yet. Did get up to a max-contig size of 95k. | + | * velvet-assembly2/ Assembling Pog Solid mate-paired 25b reads with velvet in double-encoded colorspace (24 DE base reads). Not had time to optimize parameters yet. Did get up to a max-contig size of 95k. |
| * velveth_de out 21 -shortPaired /campusdata/BME235/data/Pog/solid_run/paired/output/doubleEncoded_input.de | * velveth_de out 21 -shortPaired /campusdata/BME235/data/Pog/solid_run/paired/output/doubleEncoded_input.de | ||
| * velvetg_de out -exp_cov 50 -cov_cutoff 13 -ins_length 2200 | * velvetg_de out -exp_cov 50 -cov_cutoff 13 -ins_length 2200 | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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