I wanted to know how much variation there is between adapter trimming programs and if I need to compare them on my genomes or if there is a well-accepted "best" program for my genome type.
So far I have been using Trimmomatic, my genomes are 45Mb fungi (basidiomycota, agaricales). My higher coverage genomes (>80X) have >90% reads surviving, but my lower coverage genomes (30-50X) drop to as low as 66% reads surviving.
Is this program sufficient or is there a significantly better program I should use?
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