Question: Hybrid assembly PacBio Illumina in 2018 ?
0
gravatar for Picasa
2.6 years ago by
Picasa550
Picasa550 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 15 months ago by pkfsantos0 • written 2.6 years ago by Picasa550

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 2.6 years ago by jean.elbers1.4k

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 2.6 years ago • written 2.6 years ago by Picasa550
0
gravatar for jon.brate
2.6 years 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 2.6 years ago • written 2.6 years ago by jon.brate250

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

ADD REPLYlink written 2.6 years ago by Picasa550

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 2.6 years ago by lieven.sterck8.5k

Thanks, I'll check it out

ADD REPLYlink written 2.6 years ago by jon.brate250

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

ADD REPLYlink written 2.1 years ago by Ric300
0
gravatar for pkfsantos
15 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 15 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 12 months ago by osowiecki0
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