Is Flash with default settings fine?
Hello,
I ran Flash on numerous fastq samples, going on to use them in QIIME, and generating a biom file. However, I have now realised that I used default settings and did not use -M 300 & -t 8, so my maximum overlap was much lower. Can someone please give me some insights into how significant this is for further results, and whether I should re-do all the samples?
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Give BBMerge.sh from BBMap a try. @Brian has a good comparison between BBMerge, FLASH and other programs that you can take a look at.