Question: MatePair de novo assembly
gravatar for alexandra.auz
4.1 years ago by
alexandra.auz20 wrote:

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.

illumina iontorrent matepair • 1.4k views
ADD COMMENTlink modified 3.9 years ago • written 4.1 years ago by alexandra.auz20

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.

ADD REPLYlink written 4.0 years ago by Asaf8.0k

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

ADD REPLYlink written 3.9 years ago by alexandra.auz20

Please use ADD COMMENT/ADD REPLY when responding to existing posts. SUBMIT ANSWER for new answers to original question.

ADD REPLYlink written 3.9 years ago by genomax85k

what is your organism

ADD REPLYlink written 3.9 years ago by Picasa530

It is a bacteria....

ADD REPLYlink written 3.8 years ago by alexandra.auz20
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