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Benchmarking Hi-C Scaffolders

This repository contains all the scripts used to benchmark popular Hi-C scaffolders. As part of the study, we created docker containers of Lachesis, HiRise, 3d-dna, and Salsa.

Align

python main/submit.py \
    --assembly assembly.fasta \
    --read-1 R1.fastq.gz \
    --read-2 R2.fastq.gz

Downsample

python main/submit.py \
    --assembly assembly.fasta \
    --coverage 100

Scaffold

python ~/scripts/main/submit.py \
    --assembly assembly.fasta \
    --reference reference.fasta \
    --coverage 100 \
    --method 3d-dna