Hybrid assembly PacBio Illumina in 2018 ?

Question

[Picasa]

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.

[jean.elbers]

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?

[Picasa]

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.

Answer 1

[jon.brate]

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

[Picasa]

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

[lieven.sterck]

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?

[jon.brate]

Thanks, I'll check it out

[Ric]

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

Answer 2

[pkfsantos]

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.

[osowiecki]

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.