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archive:computer_resources:assemblies [2011/06/03 15:40]
karplus [slug/] added more on mitochondrion assembly
archive:computer_resources:assemblies [2011/06/21 23:27]
karplus [slug/] moved mitochondrion assembly information to a new page
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     * so ran with filling -R to get 12k maxcontig.     * so ran with filling -R to get 12k maxcontig.
     * Then ran the scaffolding steps with 200bp insert size.     * Then ran the scaffolding steps with 200bp insert size.
-    * For all steps, used low default cutoffs since our 10x coverage +    * For all steps, used low default cutoffs since our 10x coverage is not high.  21k max scaffold size.   
-    * is not high.  21k max scaffold size.  ​Estimated +    * Estimated ​genome size is around 3G.  ​ 
-    * genome size is around 3G.  The 4 steps are+    * The 4 steps are
       - pregraph (3.5 to 4.5 hours for 30 to 60 cpus)       - pregraph (3.5 to 4.5 hours for 30 to 60 cpus)
       - contig (1.3 hours)       - contig (1.3 hours)
       - map (0.6 hours with 60cpus) - paired ends       - map (0.6 hours with 60cpus) - paired ends
       - 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)]] +  * barcode-of-life/​ attempt to assemble the mitochondrial genome, ​documented ​on its own page: [[computer_resources:assemblies:​mitochondrion]] 
-      * 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-assembly2/​ Assembly with new + old Illumina and 454 data.
     * SOAPdenovo 1.05 - can handle gzipped fastq files.     * SOAPdenovo 1.05 - can handle gzipped fastq files.
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       - scaff:       - scaff:
         * intra-scaffold gap closure on (-F)         * 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
 +
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31