Error correction with Illumina

[mictadlo]

Hi,
New tools have been published for error correcting PacBio reads with Illumina reads:

• HALC (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1610-3 )
• FMLRC (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807796)

I am just wondering which tool do you think is the best one because currently to do error correcting our reads takes a long time.

Thank you in advance,

Michal

[pb-cdunn]

Would you be error-correcting the Falcon preads, or the Falcon draft assembly? Or is this meant to error-correct the subreads, to provide preads as input to Falcon?

[mictadlo]

I was thinking about the raw reads (subreads) but if it possible also to correct Falcon preads then I could correct it, too.

After Falcon we would like to run Falcon_unzip and Falcon-phase. If it would help to correct the assemblies between Falcon and Falcon_unzip or Falocon_unzip and Falcon-phase as well then we could do it, too.

Thank you in advance,

Michal