archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2011/06/08 05:59] karplus [slug/] fixed bullets in SOAPdenovo assembly 1 |
archive:computer_resources:assemblies [2011/06/08 15:47] karplus [slug/] added info about abyss iteration and bwa+samtools+bcftools |
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| * Iterating mapping reads with BWA and assembling them with SOAPdenovo made some progress, but there was a gap that just wouldn't close. | * 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). | * 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). | ||
| + | * Iterating search and abyss assembly does not lengthen the large contig. Cleaning up and calling the consensus with bwa+samtools+bcftools doesn't change things much either. There seems to be a large variation in coverage (from 20x to 2300x, with a median of 225x), so I suspect that there is a repeat region at the beginning of the current contig that may have 10 repeats in it. | ||
| * 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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