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archive:computer_resources:assemblies [2010/06/12 02:14] mpcusack |
archive:computer_resources:assemblies [2011/06/07 23:16] karplus [slug/] added abyss assembly info to barcode-of-life |
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* 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. | ||
+ | * Iterating mapping reads with BWA and assembling them with SOAPdenovo made some progress, but there was a gap that just wouldn't close. | ||
+ | * Switching to abyss (version 1.2.7) for the assembly of the reads made a much larger contig (15535-long after pasting on a suggestion from one abyss assembly onto another). | ||
+ | * 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: | ||
+ | * 1,298,372 scaffolds from 4,814,226 contigs sum up 632,702,276bp, with average length 487, 0 gaps filled | ||
+ | * 3,611,844 scaffolds&singleton sum up 1,133,413,022bp, with average length 313 | ||
+ | * the longest is 10,340bp,scaffold N50 is 442 bp, scaffold N90 is 148 bp | ||
+ | * k47: | ||
+ | * 871,819 scaffolds from 5,306,463 contigs sum up 530,762,874bp, with average length 608, 0 gaps filled | ||
+ | * 4,203,195 scaffolds&singleton sum up 1,296,678,043bp, with average length 308 | ||
+ | * the longest is 14,750bp,scaffold N50 is 458 bp, scaffold N90 is 140 bp | ||
+ | * k63: | ||
+ | * 270,887 scaffolds from 4,022,505 contigs sum up 139,720,415bp, with average length 515, 0 gaps filled | ||
+ | * 3,710,532 scaffolds&singleton sum up 690,332,560bp, with average length 186 | ||
+ | * the longest is 14,897bp,scaffold N50 is 232 bp, scaffold N90 is 112 bp | ||