workflow for hifiasm assembly stuff
Hifiasm is used for assembling DNA sequences. It was originally developed for assembling sequences from PacBio HiFi reads, but the latest version can also assemble sequences from ultralong Oxford Nanopore reads. Hifiasm is particularly useful for producing high-quality assemblies that accurately represent the two copies of each chromosome in an organism's genome. This is achieved by using parental short reads or Hi-C data to help resolve differences between the two copies.
Code Snippets
51 | shell: "hifiasm/hifiasm -o " + out_pre +".{wildcards.s_par} -s {wildcards.s_par} -t {threads} --primary {input}" |
57 | shell: "awk \'/^S/{{print \">\"$2\"\\n\"$3}}\' {input} | fold | gzip > {output}" |
63 | shell: "assembly-stats {input} > {output}" |
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Created: 1yr ago
Updated: 1yr ago
Maitainers:
public
URL:
https://github.com/andrewkern/octo_snakemake
Name:
octo_snakemake
Version:
1
Downloaded:
0
Copyright:
Public Domain
License:
MIT License
Keywords:
- Future updates
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