archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2010/04/22 13:28] karplus corrected order of short repeats (using double-stranded counts) |
archive:computer_resources:assemblies [2010/04/22 13:43] karplus moved velvet-assembly1 to test |
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| ====== assemblies/ ====== | ====== assemblies/ ====== | ||
| This directory has a subdirectory for each organism. | This directory has a subdirectory for each organism. | ||
| + | |||
| + | ===== test/ ===== | ||
| + | |||
| + | For test assemblies provided by the tool makers to check that installation is correct. | ||
| + | * velvet | ||
| + | * velvet-assembly1/ A first attempt to use velvet to assemble its own simulated TEST 100kb genome with short 35b reads and long 100b reads. Assembly worked very well in the end. Was reminded that when using short reads, must keep k small to get adequate coverage. | ||
| + | * 6th try, k=21 cov=19 -shortPaired -long | ||
| + | * Final graph has 9 nodes and n50 of 99975, max 99975, total 100143, using 137863/144858 reads | ||
| + | * RESULTS: excellent! (TEST DATA ONLY) | ||
| + | |||
| ===== Pog/ ===== | ===== Pog/ ===== | ||
| Line 20: | Line 30: | ||
| * mira | * mira | ||
| * mira-assembly1/ | * mira-assembly1/ | ||
| - | * velvet | + | |
| - | * velvet-assembly1/ A first attempt to use velvet to assemble its own simulated TEST 100kb genome with short 35b reads and long 100b reads. Assembly worked very well in the end. Was reminded that when using short reads, must keep k small to get adequate coverage.\\ | + | * 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:\\ |
| - | * 6th try, k=21 cov=19 -shortPaired -long\\ | + | |
| - | * Final graph has 9 nodes and n50 of 99975, max 99975, total 100143, using 137863/144858 reads\\ | + | |
| - | * RESULTS: excellent! (TEST DATA ONLY)\\ | + | |
| - | * 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:\\ | + | |
| * 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-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. | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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