denovo assembly combining multiple data sets

Question

[slimane.khayi]

Dear guys We ave sequenced the whole genome of a plant species (about 700Mb) using two technologies and the data output as bellow:

Illumina: PE 2*150, insert size 330-550bp, random sharing total reads : 606 037 434 total bases: 91 511 652 534 (90Gb)

IonTorrent : single read, average lenght 125bp, enzymatique sharing, total reads : 247 000 000 total bases : ~ 20 000 000 000 (20Gb)

My questions are : can we perform a denovo assembly? have you a methodological proposal to optimise the assembly (combining these two data sets ? Which software you suggest to use? Thank you i advance for you help! have a nice day to all.

Answer 1

[colindaven]

Soapdenovo2 would be useful for this as it allows simple use of different libraries (if you want to do this).

I don't think the Ion Torrent reads are going to help at all though, since they are a shorter read length and not paired end. To my knowledge they also contain a lot of indel errors, which are awful for assemblies.

Remember to trim your Illumina reads before assembling.

Answer 2

[Tm]

SOAPdenovo2 is a good choice. You can also try velvet and newbler which gives you option of considering reference genome as input and provides reference guided assembly

Answer 3

[slimane.khayi]

thankyou colindaven, I'll try with Soapdenovo. What about if I want to perform a denovo using a reference? thanks.

Answer 4

[slimane.khayi]

Thank you colindaven for your reactivity.