Question: Hybrid assembly PacBio Illumina in 2018 ?
0
gravatar for Picasa
20 months ago by
Picasa470
Picasa470 wrote:

Hi,

Do you have any recommendation for a hybrid assembly of a 1.5G diploid genome using Illumina and Pacbio reads ?

I have different insert size libraries with Illumina (paired end and mate pair).

I ve seen this page

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Large-Genome-Assembly-with-PacBio-Long-Reads

but last update was in 2016 so I am not sure whether it is up to date anymore.

Thanks for your help.

ADD COMMENTlink modified 4 months ago by pkfsantos0 • written 20 months ago by Picasa470

What sequencing coverage do you have for the PacBio reads? Are they from the RSII or Sequel? What sequencing coverage do you have for the Illumina paired end reads? What are the insert sizes for the mate pair libraries?

ADD REPLYlink written 20 months ago by jean.elbers1.3k

Thanks for your answer jean.

PacBio data: Sequel and coverage 20X

Illumina data: Total coverage 50X and Insert size: 350, 550, 700 for PE and 3000, 5000 for MP.

ADD REPLYlink modified 20 months ago • written 20 months ago by Picasa470
0
gravatar for jon.brate
20 months ago by
jon.brate250
Norway
jon.brate250 wrote:

Facing some of the same issues myself these days and looking forward to read the responses. Currently we are using the following pipeline (eukaryotic genome):
1. Correct PacBio reads with LoRDEC using the Illumina reads
2. Assemble the corrected PacBio reads using Canu
3. Running Spades on the Illumina reads toghether with the Canu assembly as trusted contigs
4. Polishing the assembly with Pilon

ADD COMMENTlink modified 20 months ago • written 20 months ago by jon.brate250

SPAdes is not really designed for medium, big genome ( > 500Mbp) from what I know.

ADD REPLYlink written 20 months ago by Picasa470

indeed.

you can give MaSuRCA a try perhaps? or Canu with PacBio, any short read assembler on the illumina and combine/scaffold both afterwards with something like MeDuSa or such?

ADD REPLYlink written 20 months ago by lieven.sterck6.0k

Thanks, I'll check it out

ADD REPLYlink written 20 months ago by jon.brate250

Try out dbg2olc (https://github.com/yechengxi/DBG2OLC)

ADD REPLYlink written 14 months ago by Ric280
0
gravatar for pkfsantos
4 months ago by
pkfsantos0
pkfsantos0 wrote:

My best results were using Pacbio corrected by Canu and a hybrid assembly using the cleaned data from illumina and the corrected Pacbio in the Masurca software.

ADD COMMENTlink written 4 months ago by pkfsantos0

https://github.com/alekseyzimin/masurca

IMPORTANT! Do not use third party tools to pre-process the Illumina data before providing it to MaSuRCA, unless you are absolutely sure you know exactly what the preprocessing tool does. Do not do any trimming, cleaning or error correction. This will likely deteriorate the assembly.

ADD REPLYlink written 6 weeks ago by osowiecki0
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