Which FLASH parameters to use?

Question

[Elisa]

Hello everyone!

I am using FLASH for merging data. I wanted to find more information about this tool but it was not possible :/

Which is the impact of using higher values of M? As soon as I know, flash did not count "N" and insert or delection as a missmatch. If this M is tooo high, can I have merged sequences that they should not match?

[GenoMax]

Not answering your question but you may want to try bbmerge.sh from BBMap suite as an alternative. Clear options and a guide available : https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbmerge-guide/