Hifiasm

Hifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads. It also supports telomere-to-telomere assembly by using ultra long Oxford Nanopore reads.

To load Hifiasm on to Palmetto 2:

module load biocontainers
module load hifiasm

For input it expects a .fq file of your reads.

tip

This software has a -t option for additional threads! Please try using additional threads when using this software to speed up your analysis.

Its usage looks roughly like:

hifiasm -o OUTPUT.asm -t 32 INPUT.fq.gz

For more information please see their official documentation.

Parallel Capabilities: Multithreading options available.