denovo assembly combining multiple data sets
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Entering edit mode
6.9 years ago

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.

denovo paired-end single-end illumina IonTorrent • 1.9k views
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6.9 years ago

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.

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6.9 years ago
Tm ★ 1.1k

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

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6.9 years ago

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

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6.9 years ago

Thank you colindaven for your reactivity.

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