INTRO

Steven asked the I assemble sea lice PacBio data using hifiasm (GitHub Issue).

I assembled the PacBio HiFi reads for the C. rogercresseyi Macho sample using hifiasm on Hyak using our Apptainer image: srlab-R4.4-bioinformatics-container-c3d3116.sif. Assembly took ~19hrs, which was significantly longer then the Hembra assembly (1.5hrs) (Notebook entry).

Now that both assemblies are complete, I’ll compare the two assemblies using QUAST.

RESULTS

Output directory:

https://gannet.fish.washington.edu/Atumefaciens/20260519-crog-macho-genome_assembly-hifiasm/

Assembly FastA:

https://gannet.fish.washington.edu/Atumefaciens/20260519-crog-macho-genome_assembly-hifiasm/crog-macho-pb-hifiasm-assembly.fa (1009MB)

VARIABLES

Code

# DIRECTORIES
data_dir <- "/mmfs1/gscratch/scrubbed/samwhite/data/C_rogercresseyi/HIFI_Caligus/Macho_01_cell1/"
output_dir <- "/mmfs1/gscratch/scrubbed/samwhite/outputs/20260519-crog-macho-genome_assembly-hifiasm/"

# FILES
hifiasm_asm <- "crog-macho-pb-hifiasm-assembly.asm"
hifiasm_primary_graph <- "crog-macho-pb-hifiasm-assembly.asm.bp.p_ctg.gfa"
hifiasm_assembly_fasta <- "crog-macho-pb-hifiasm-assembly.fa"
hifiasm_assembly_log <- "crog-macho-pb-hifiasm-assembly.log"

# PROGRAMS
gfatools <- c("/srlab/programs/gfatools/gfatools")
hifiasm <- c("/srlab/programs/miniforge3-24.7.1-0/envs/hifiasm-0.25.0_env/bin/hifiasm")


# SETTINGS
threads <- "50"


# Export these as environment variables for bash chunks.
Sys.setenv(
  data_dir = data_dir,
  gfatools = gfatools,
  hifiasm = hifiasm,
  hifiasm_asm = hifiasm_asm,
  hifiasm_assembly_fasta = hifiasm_assembly_fasta,
  hifiasm_assembly_log = hifiasm_assembly_log,
  hifiasm_primary_graph = hifiasm_primary_graph,
  output_dir = output_dir,
  threads = threads
)

HIFIASM

Code

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

cd "${output_dir}"

# Create an array of .fastq.gz files
fastqs=(${data_dir}/*.fastq.gz)

# Print the result (optional, for verification)
## newline-delimited format
echo "List of FastQs used for assembly:"

printf "%s\n" "${fastqs[@]}" \
| tee input_fastqs.txt

# Run hifiasm assembly
"${hifiasm}" \
-o "${hifiasm_asm}" \
-t "${threads}" \
"${fastqs[@]}" \
> "${hifiasm_assembly_log}" 2>&1

3 GFATOOLS

3.1 Primary contigs to FastA

This will extract a FastA file from the graph files output by hifiasm.

Code

cd "${output_dir}"

"${gfatools}" gfa2fa \
"${hifiasm_primary_graph}" \
> "${hifiasm_assembly_fasta}"

samtools faidx "${hifiasm_assembly_fasta}"

CHECKSUMS

Code

cd "${output_dir}"

for fasta in *.fa
do
  md5sum "${fasta}" \
  | tee "${fasta}".md5
done