hifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads. hifiasm-docker provides Docker files and GitHub Action workflows for building and publishing a Docker image so that hifiasm can be used in the sync-seq workflow.

sync-seq provides a Nextflow workflow encapsulating the computational components to take output from the 15:1 molar libraries of gDNA:cDNA sequenced on the PacBio Revio following the protocols published by Vollger, Mitchell R., Jonas Korlach, Kiara C. Eldred, Elliott Swanson, Jason G. Underwood, Yong-Han H. Cheng, Jane Ranchalis, et al. 2023. “Synchronized Long-Read Genome, Methylome, Epigenome, and Transcriptome for Resolving a Mendelian Condition.” Preprint. Genetics. https://doi.org/10.1101/2023.09.26.559521.

To build your image from the command line:

• You can do this on Google shell since docker is installed and available.

docker build -t hifiasm:latest .

To test this tool from the command line:

docker run -it hifiasm:latest hifiasm -h

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