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vpc-ccg / haslr

A fast tool for hybrid genome assembly of long and short reads
GNU General Public License v3.0
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Using CCS/HiFi PacBio reads #6

Closed mbhall88 closed 4 years ago

mbhall88 commented 4 years ago

Is there anything "wrong" with me using CCS reads for the long reads? i.e. is there some kind of inferred error rate attached to the long reads parameter that will mess this up? (CCS reads have a very low error rate compared to raw ont/pacbio)

haghshenas commented 4 years ago

Hi Michael,

There is nothing wrong with using HiFi long reads. But we might get too many alignments when aligning short read contigs to long reads using either -x pacbio or -x nanopore. I need to make another option for these reads.

haghshenas commented 4 years ago

I added the experimental option -x corrected. It employs minimap2 with a larger k-mer size compared to -x pacbio and -x nanopore.

haghshenas commented 4 years ago

Remember that before I update the bioconda recipe, in order to get the latest changes, you need to build HASLR from source (check here) rather than using the bioconda version. The bioconda recipe will be updated after releasing a new tag.

mbhall88 commented 4 years ago

When you say -x pacbio are you referring to minimap2 params? If so, there is a preset for CCS reads -x asm20.

haghshenas commented 4 years ago

Not exactly. It doesn't pass the same parameter to minimap2.

mbhall88 commented 4 years ago

Great! I'll give it a try either today or tomorrow.

For my own interest, how come you don't use the presets for the different technologies?