Hifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads. Its latest release supports telomere-to-telomere assembly by utilizing ultralong Oxford Nanopore reads. It can produce better haplotype-resolved assemblies when given parental short reads or Hi-C data.

References:

• Cheng, H., Concepcion, G.T., Feng, X., Zhang, H., Li H. (2021) Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods, 18:170-175. doi:10.1038/s41592-020-01056-5
• Cheng, H., Jarvis, E.D., Fedrigo, O., Koepfli, K.P., Urban, L., Gemmell, N.J., Li, H. (2022) Haplotype-resolved assembly of diploid genomes without parental data. Nature Biotechnology, 40:1332–1335. doi:10.1038/s41587-022-01261-x

• hifiasm Main Site
• hifiasm on GitHub

• Module Name: hifiasm (see the modules page for more information)
• Multithreaded. Set number of threads with the -t flag

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task 32
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load hifiasm

[user@cn3144 ~]$ hifiasm -t $SLURM_CPUS_PER_TASK -o NA24385_180901_0113427.asm /fdb/app_testdata/fastq/Homo_sapiens/HG002_NA24385_son-PacBio_CCS_15kb/m54238_180901_011437.Q20.fastq.gz

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. hifiasm.sh). For example:

#!/bin/bash
set -e
module load hifiasm
hifiasm -t $SLURM_CPUS_PER_TASK -o NA24385_180901_0113427.asm /fdb/app_testdata/fastq/Homo_sapiens/HG002_NA24385_son-PacBio_CCS_15kb/m54238_180901_011437.Q20.fastq.gz

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=# [--mem=#] hifiasm.sh

Create a swarmfile (e.g. hifiasm.swarm). For example:

hifiasm -t $SLURM_CPUS_PER_TASK -o sample1.asm sample1.fq.gz
hifiasm -t $SLURM_CPUS_PER_TASK -o sample2.asm sample2.fq.gz
hifiasm -t $SLURM_CPUS_PER_TASK -o sample3.asm sample3.fq.gz
hifiasm -t $SLURM_CPUS_PER_TASK -o sample4.asm sample4.fq.gz

Submit this job using the swarm command.

swarm -f hifiasm.swarm [-g #] -t # --module hifiasm