search

kensung-lab / hypo-assembler

37 stars 3 forks source link

Input reads and outputs #13

Open OZTaekOppa opened 6 months ago

OZTaekOppa commented 6 months ago

Thank you for creating such a great program.

After reviewing the manual, I have a few questions regarding its usage and options:

  1. For "-l ", can we only use reads from a single platform (e.g., PacBio HiFi or ONT Ultra-Long read), or is it possible to combine reads from multiple platforms?

  2. Regarding "-d ", I've produced phased-haplotype assemblies, hap1.fa and hap2.fa, using hifiasm. Can the program only process one, like hap1.fa, or can it handle multiple haplotype fasta files?

  3. For "-o ", this is related to "-d ". If Hapo-Assembler only takes a single hap1.fa for "-d ", it generates _1.fa and _2.fa as outputs. If it could handle multiple haplotype fasta files, how would the outputs be named?

I appreciate your guidance on these questions.

Thanks!

Taek

joshua-casey commented 6 months ago

Hi Taek,

Thank you for your interest in hypo-assembler.

  1. Currently, hypo-assembler is only designed for ONT long reads. In the algorithm, HiFi reads takes more of the place of the short reads, but it is currently unimplemented since the short reads expects paired-end.
  2. Currently it processes one. Given just one haplotpye input though, we expect to produce both haplotypes.

Thank you. Sincerely, Joshua Casey Darian