Salsa in Docker

Salsa is a popular Hi-C scaffolding method. The container is available via Docker Hub.

Usage

# Index assembly.
samtools faidx \
    assembly.fasta

# Bam to bed. 
bedtools bamtobed \
    -i alignment.bam | \
    sort -k 4 > \
    alignment.bed

# Pull image. 
docker pull \
  aakashsur/salsa

# Run salsa.
docker run \
  --rm \
	--volume $PWD:/root/results \
	--workdir $PWD:/root/results \
	aakashsur/salsa \
	salsa \
	-a assembly.fasta \
	-l assembly.fasta.fai \
	-b alignment.bed \
	-e GATC \
	-o scaffolds

Details

The salsa command has been placed in $PATH. Salsa requires an index of the assembly, and a conversion of the alignment bam file into a bed file. Once those are in place, you can run the command and scaffold your assembly.

To build from scratch -

docker build \
  -t username/salsa:latest \
  path_to_dockerfile

For running in an HPC setting, where singularity is often the choice of containerization -

singularity pull \
  docker://aakashsur/salsa
  
singularity run \
	--bind $PWD:/root/results \
	--home $PWD:/root/results \
	~/software/salsa/salsa_latest.sif \
	salsa \
	-a assembly.fasta \
	-l assembly.fasta.fai \
	-b alignment.bed \
	-e GATC \
	-o scaffolds