Salsa is a popular Hi-C scaffolding method. The container is available via Docker Hub.
# 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
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
Content type
Image
Digest
Size
221.8 MB
Last updated
about 5 years ago
docker pull aakashsur/salsa