archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2010/04/22 20:25] karplus added newbler mapping assemblies |
archive:computer_resources:assemblies [2010/04/30 23:01] karplus added mention of trim9.joins for the homework. |
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| * newbler-assembly4/ starts from the same sff file as newbler-assembly2/ and newbler-assembly3/ but adds the contigs of newbler-partial3/ as extra reads. This did not help, getting 45 contigs and 2,449,287 bases. | * newbler-assembly4/ starts from the same sff file as newbler-assembly2/ and newbler-assembly3/ but adds the contigs of newbler-partial3/ as extra reads. This did not help, getting 45 contigs and 2,449,287 bases. | ||
| * newbler-assembly5/ starts from the same sff file as newbler-assembly2,3,4 but adds 45 Sanger reads totalling 44,187 bases from PCR reactions (mainly designed to test contig-join hypotheses). It gets 31 contigs and 2,451,007 bases. | * newbler-assembly5/ starts from the same sff file as newbler-assembly2,3,4 but adds 45 Sanger reads totalling 44,187 bases from PCR reactions (mainly designed to test contig-join hypotheses). It gets 31 contigs and 2,451,007 bases. | ||
| - | * map-colorspace5/ maps the SOLiD mate-pair data onto the contigs of newbler-assembly5/ Other than some problems placing contig4 and the ece insertions, we can reconstruct some pretty large chunks of the genome from the mate-pair ends. | + | * map-colorspace5/ maps the SOLiD mate-pair data onto the contigs of newbler-assembly5/ Other than some problems placing contig4 and the ece insertions, we can reconstruct some pretty large chunks of the genome from the mate-pair ends. This directory contains the trim9.joins file, which is needed for doing the **homework** to attempt to reconstruct the genome. |
| * euler | * euler | ||
| * euler-assembly1/ | * euler-assembly1/ | ||
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| * mira | * mira | ||
| * mira-assembly1/ | * mira-assembly1/ | ||
| - | + | * velvet | |
| - | * 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 2176 nodes {195 contigs over 62b) and n50 of 224364, max {contig size} 680241, total {genome size} 2481051, using 778249/782604 reads |
| - | * 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 | ||
| Line 43: | Line 43: | ||
| ===== slug/ ===== | ===== slug/ ===== | ||
| * newbler-assembly1/ first attempt at de novo assembly using Newbler, using all the reads from 454_run1 and 454_run2. | * newbler-assembly1/ first attempt at de novo assembly using Newbler, using all the reads from 454_run1 and 454_run2. | ||
| - | * This assembly of 499,873 reads including 138,351,643 bases produced only 2,910,773 bases assembled into 8,963 contigs. | + | * This assembly of 499,873 reads including 138,351,643 bases produced only 2,910,773 bases assembled into 8,963 contigs. |
| - | * From this low assembly number, I estimate the coverage to be about 0.043x and the genome size to be about 3.2E9 basepairs. (See the README file for the calculation.) | + | * The longest contig is 5783 bases. |
| + | * From the total number of bases in the assembly number, I estimate the coverage to be about 0.043x and the genome size to be about 3.2E9 basepairs. (See the README file for the calculation.) | ||
| * Much of the assembly is low-complexity regions (repetitions of short repeats (AT)*, (AAG)*, (AG)*, (AC)*, (AGT)*, (AGAT)*, (ACAT)*, (AAC)*, (AACG)*, ... ). | * Much of the assembly is low-complexity regions (repetitions of short repeats (AT)*, (AAG)*, (AG)*, (AC)*, (AGT)*, (AGAT)*, (ACAT)*, (AAC)*, (AACG)*, ... ). | ||
| * The most common 14-mer that is not a repeat of a short k-mer is TAGTTTACAGCTTG (so that is what we should put on the T-shirt). | * The most common 14-mer that is not a repeat of a short k-mer is TAGTTTACAGCTTG (so that is what we should put on the T-shirt). | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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