I'm sharing my automation of the Juicer/3D_DNA and SALSA Hi-C scaffolding pipelines.
Juicer maps HiC reads to an input assembly. Use:
run_juicer.sh < input_assembly.fasta > < project name >
You need to edit the following variables with your own directory of installed juicer and 3D-DNA:
JUICERDIR="/../scaffolding/juicer/00_juicer"
VIZ_DIR="/../scaffolding/juicer/01_3D-DNA/visualize/visualizations"
You also need to create a folder called fastq in 00_juicer with the soft links of HiC_R1.fastq and HiC_R2.fastq.
You can scaffold the resulting Juicer project with 3D-DNA. Use:
run_3d-dna.sh < project name >