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novi 06-30-2011 02:28 AM

downsampling high coverage regions in SAGs

I am working with single cell amplified genomes (SAGs), which leads to a very uneven distribution of reads among the genome; some regions will have extremely high coverage and some extremely low. To make better assemblies, it is required that the high coverage are 'downsampled', i.e. discarding reads in a high coverage region until that region reaches a certain coverage. This would then ultimately lead to a more uniform coverage, easing the assembly.

Is there some way or script to do this? I use velvet as assembler.

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