archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2010/06/09 19:13] svasili |
archive:computer_resources:assemblies [2011/06/03 21:37] eyliaw [slug/] |
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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 102: | Line 103: | ||
| * is not high. 21k max scaffold size. Estimated | * is not high. 21k max scaffold size. Estimated | ||
| * genome size is around 3G. The 4 steps are | * genome size is around 3G. The 4 steps are | ||
| - | * 1. pregraph (3.5 to 4.5 hours for 30 to 60 cpus) | + | - pregraph (3.5 to 4.5 hours for 30 to 60 cpus) |
| - | * 2. contig (1.3 hours) | + | - contig (1.3 hours) |
| - | * 3. map (0.6 hours with 60cpus) - paired ends | + | - map (0.6 hours with 60cpus) - paired ends |
| - | * 4. scaff (1 hour with 60cpus) | + | - scaff (1 hour with 60cpus) |
| + | * barcode-of-life/ attempt to assemble the mitochondrial genome, with particular emphasis on the gene for mitochondrial cytochrome c oxidase subunit I protein I (CO1), which is used for the "barcode of life". [[http://www.boldsystems.org/|BOLD (barcode of life database)]] | ||
| + | * Started with a search of SOAPdenovo-assembly1/k31/soapSlug.scafSeq for scaffolds that matched examples from other mollusks. | ||
| + | * Looked for 454 reads that extended or joined contigs in scaffold | ||
| + | * Repeated (sometimes using more sensitive searches) until no more credible scaffolds from the SOAPdenovo-assembly1/k31/ assembly nor 454 reads were found. | ||
| + | * The 454 coverage of the mitochondrion is so slight as to be nearly useless, so instead we can iterate: | ||
| + | - find all Illumina reads that map to the mitochondrial draft, using BWA | ||
| + | - assemble them using SOAPdenovo. | ||
| + | * It looks like the Illumina reads have about 228x coverage of the mitochondrion, but coverage is patchy, and it seems to be difficult to close the circle (at least with SOAPdenovo). | ||
| + | * We have an almost complete mitochondrial genome, and I'm hoping that a few more iterations or some tricky assembly will close it into a clean circular genome. | ||
| + | * It turns out that a lot of the hard hand work and iterated searching to assemble the mitochondrion was not necessary, as the SOAPdenovo-assembly2/k63_w_454_contigs/ assembly now has a 14960-long contig (not scaffold!) which is an almost-full-length mitochondrion, roughly as good as the best I've managed to assemble so far. I'll combine it with my efforts and see if I can eke out a few more bases. | ||
| + | * SOAPdenovo-assembly2/ Assembly with new + old Illumina and 454 data. | ||
| + | * SOAPdenovo 1.05 - can handle gzipped fastq files. | ||
| + | * Runs with k27, 31, 47, and 63 so far. 47 was the best overall. 63 got the longest contig (~14.9kb). | ||
| + | * Run parameters: | ||
| + | - pregraph: | ||
| + | * lowest count size of 2 (-d 2) | ||
| + | - contig: | ||
| + | * solve tiny repeats on (-R) | ||
| + | - map: | ||
| + | * all default | ||
| + | - scaff: | ||
| + | * intra-scaffold gap closure on (-F) | ||
| + | * Statistics for each kmer size assembly (using illumina and 454 data, using both for contig and scaffolding): | ||
| + | * k31: | ||
| + | 1298372 scaffolds from 4814226 contigs sum up 632702276bp, with average length 487, 0 gaps filled | ||
| + | 3611844 scaffolds&singleton sum up 1133413022bp, with average length 313 | ||
| + | the longest is 10340bp,scaffold N50 is 442 bp, scaffold N90 is 148 bp | ||
| + | * k47: | ||
| + | 871819 scaffolds from 5306463 contigs sum up 530762874bp, with average length 608, 0 gaps filled | ||
| + | 4203195 scaffolds&singleton sum up 1296678043bp, with average length 308 | ||
| + | the longest is 14750bp,scaffold N50 is 458 bp, scaffold N90 is 140 bp | ||
| + | * k63: | ||
| + | 270887 scaffolds from 4022505 contigs sum up 139720415bp, with average length 515, 0 gaps filled | ||
| + | 3710532 scaffolds&singleton sum up 690332560bp, with average length 186 | ||
| + | the longest is 14897bp,scaffold N50 is 232 bp, scaffold N90 is 112 bp | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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