help to do genome assembly

[wanadou]

I prepare genomic shotgun libraries for sequencing using Single Molecule Real Time (SMRT) sequencing platform produced by PacBio (20X coverage of PacBio reads) coupled with sequencing on Illumina platform (30X coverage of Illumina Miseq 250bp reads).The obtained data will be used to perform a de novo hybrid assembly by combining both Illumina and PacBio reads to generate accurate draft assemblies of plant genome (with estimated size of 350 Mbp).

1- What types of assembler I should use?

2-A computer equipped with 320 RAM, 3TB hard disc and 2 x Xeon 2680v2 is it sufficient to analyze the results of sequencing and to make a hybrid assembly?

[wkusmire]

Hi, I think that the computer you have is sufficient. I suggest you to do firstly de novo assembly of your Illumina reads and then links obtained sequences using PacBio reads. For Illumina reads I can recommend you ABySS, Velvet and SOAPdenovo assemblers. However, it is also valuable to check, if in your genome long tandem repeats are present. To do that, I recommend dnaasm de novo assembler (I'm an author of this application). It has also a module to linkage contigs by your long reads - for the second step of your analysis. If you have any questions fell free to contact me

How many Illumina reads do you have?

[jgibbons1]

Try assembling raw PacBio reads with Canu, then polish the assembly using the Illumina reads with Pilon.

[wkusmire]

I think that 20x PacBio won't be enough for Canu de novo assembler, but you can try of course

[wanadou]

Thanks wkusmire and jgibbons1 for your reply
I have not yet started sequencing but I'm getting ready to do it.
Is it possible to recommend me a company to do it?

[wkusmire]

I don't know any sequencing company, I only analyze NGS data

[SNPsaurus]

Thanks wkusmire and jgibbons1 for your reply
I have not yet started sequencing but I'm getting ready to do it.
Is it possible to recommend me a company to do it?

We use the University of Oregon sequencing facility, which has a PacBio Sequel, MiSeq and Hiseq4000. https://gc3f.uoregon.edu/