Hi-C-scaffolding-pipelines

I'm sharing my automation of the Juicer/3D_DNA and SALSA Hi-C scaffolding pipelines.

Juicer

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.

3D-DNA

You can scaffold the resulting Juicer project with 3D-DNA. Use:

run_3d-dna.sh < project name >