Hi everyone, i am having some problems with a de novo assembly. I have two MatePair files, one from Illumina MiSeQ and the other from IonTorrent. My problem is first how do i prepare the data before the assembly, and then, which assembler is better? (I have been working with Ray, MIRA, Newbler and SPAdes, these last two gave much better results in other data) In Illumina matepair, i tried to work with NxTrim but i need two files as an input and i do not know if a complementary file of the original will work, then i tried Trimmomatic too, and used these files as entrey (the original and the complementary i created) but i'm not sure if the output files will work for the assembler... Anyway, has anyone has any experience working with these kind of data? Which pipeline do you recommend? Thanks in advance.
What are you assembling? Do you have an even coverage of the genome? Are they both Mate-Pair or paired-end? IDBA-UD can handle input from different sequencing types.
Hey, thanks for the answer. It is a bacterian genome. I have even coverage. I have dataset both of Mate-Pair and Paired-End. Will give it a try. Thanks
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ADD COMMENT/ADD REPLYwhen responding to existing posts.SUBMIT ANSWERfor new answers to original question.what is your organism
It is a bacteria....