Question: Hybrid assembly PacBio Illumina in 2018 ?
0
gravatar for Picasa
14 months ago by
Picasa390
Picasa390 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 14 months ago by jon.brate200 • written 14 months ago by Picasa390

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 14 months ago by jean.elbers970

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 14 months ago • written 14 months ago by Picasa390
0
gravatar for jon.brate
14 months ago by
jon.brate200
Norway
jon.brate200 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 14 months ago • written 14 months ago by jon.brate200

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

ADD REPLYlink written 14 months ago by Picasa390

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 14 months ago by lieven.sterck4.5k

Thanks, I'll check it out

ADD REPLYlink written 14 months ago by jon.brate200

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

ADD REPLYlink written 8 months ago by Ric190
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 787 users visited in the last hour