Assembling pacbio, nanopore and illumina reads

[charles-gumbi]

Thanks for providing and maintaining HASLR. Is it possible to use HASLR to assembly sequences from pacbio, nanopore, and Illumina all together at the same time? I have used HASLR to assembly pacbio and Illumina before and it worked well. But now I have data from nanopore on the same individuals. This is a bat genome that is estimated t be at 3Gb.
Humble regards
Charles

[fhach]

Hi Charles,

Although, we have not tested the scenario you explained but I would give the ONT/PacBio together to haslr. It may work without any other modifications.

[charles-gumbi]

Hey Fhach, thank you for your swift response. I have supplied both long reads to haslr and seem to be running smoothly so far. But ill have to wait for the final assembly to access the success
below is the one of code Im running in the the server :

#running the HASLR in command line
haslr.py --type pacbio --type nanopore --out bat_genome_output --genome 3g --long pacbio_subreads.fastq --long nanopore_reads.fastq --short illumina_lane1_forward.fastq illumina_lane1_reverse.fastq llumina_lane2_forward.fastq illumina_lane2_reverse.fastq

humbles regards
charles