INTRO

I previously assembled two C. rogercresseyi genomes (Hembra and Macho) using hifiasm on Hyak:

2026-05-19-Genome-Assembly—C.rogercresseyi-Hembra-with-PacBio-HiFi-Reads-Using-hifiasm-on-Hyak (Notebook entry)
2026-05-19-Genome-Assembly—C.rogercresseyi-Macho-with-PacBio-HiFi-Reads-Using-hifiasm-on-Hyak (Notebook entry)

Used QUAST (SourceForge) to evaluate the two sets of PacBio genome assemblies produced with hifiasm (GitHub). QUAST was run on Hyak using our Apptainer image: srlab-R4.4-bioinformatics-container-c3d3116.sif.

RESULTS

Output directory:

https://gannet.fish.washington.edu/Atumefaciens/20260520-crog-quast/

Report (HTML):

https://gannet.fish.washington.edu/Atumefaciens/20260520-crog-quast/report.html

All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).

Assembly                    hembra_hifiasm  macho_hifiasm
# contigs (>= 0 bp)         38173           29083        
# contigs (>= 1000 bp)      38173           29083        
# contigs (>= 5000 bp)      38114           29063        
# contigs (>= 10000 bp)     32342           26462        
# contigs (>= 25000 bp)     9330            10803        
# contigs (>= 50000 bp)     2607            4232         
Total length (>= 0 bp)      965132142       1039559438   
Total length (>= 1000 bp)   965132142       1039559438   
Total length (>= 5000 bp)   964862679       1039469033   
Total length (>= 10000 bp)  916572303       1017589149   
Total length (>= 25000 bp)  551660840       756247282    
Total length (>= 50000 bp)  325882306       532742257    
# contigs                   38173           29083        
Largest contig              5795613         5889309      
Total length                965132142       1039559438   
GC (%)                      35.50           36.26        
N50                         29880           52326        
N90                         11881           15183        
auN                         263844.4        315728.2     
L50                         6795            3979         
L90                         27965           20005        
# N's per 100 kbp           0.00            0.00

Code is below.

SETUP

Libraries

Code

library(knitr)
library(tidyverse)

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr     1.1.4     ✔ readr     2.1.5
## ✔ forcats   1.0.0     ✔ stringr   1.5.1
## ✔ ggplot2   3.5.2     ✔ tibble    3.2.1
## ✔ lubridate 1.9.4     ✔ tidyr     1.3.1
## ✔ purrr     1.0.4     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Variables

Code

# OUTPUT DIRECTORY
output_dir <- "/mmfs1/gscratch/scrubbed/samwhite/outputs/20260520-crog-quast"

# FILES
hifiasm_hembra_fasta <- "/mmfs1/gscratch/scrubbed/samwhite/outputs/20260519-crog-hembra-genome_assembly-hifiasm/crog-hembra-pb-hifiasm-assembly.fa"
hifiasm_macho_fasta <- "/mmfs1/gscratch/scrubbed/samwhite/outputs/20260519-crog-macho-genome_assembly-hifiasm/crog-macho-pb-hifiasm-assembly.fa"
quast_log <- "/mmfs1/gscratch/scrubbed/samwhite/outputs/20260520-crog-quast/quast_log.txt"

# SETTINGS
threads <- "40"


# Export these as environment variables for bash chunks.
Sys.setenv(
  hifiasm_hembra_fasta = hifiasm_hembra_fasta,
  hifiasm_macho_fasta = hifiasm_macho_fasta,
  output_dir = output_dir,
  quast_log = quast_log,
  threads = threads
)

QUAST

Code

# Make output directory, if it doesn't exist
mkdir --parents "${output_dir}"

quast.py \
"${hifiasm_hembra_fasta}" \
"${hifiasm_macho_fasta}" \
--output-dir "${output_dir}" \
--threads "${threads}" \
--labels "hembra_hifiasm, macho_hifiasm" \
> "${quast_log}" 2>&1