archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2011/06/03 22:12] eyliaw [slug/] |
archive:computer_resources:assemblies [2011/06/07 23:16] karplus [slug/] added abyss assembly info to barcode-of-life |
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| * 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. | * 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. | * 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-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. | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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