SALSA
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marbl
SALSA: A tool to scaffold long read assemblies with Hi-C data
Hi, I am running SALSA on a GFA created by Hifiasm, but it crashed. My command line: ~/miniconda3/envs/py2.7/bin/python /public1/home/ligch/software/SALSA/run_pipeline.py -a /public1/home/ligch/Harm_Hass_genome/Harm/03_HiC_assembly/reference/Harm.primary.asm.p_ctg.fa -l /public1/home/ligch/Harm_Hass_genome/Harm/03_HiC_assembly/reference/Harm.primary.asm.p_ctg.fa.fai -b Harm.primary.alignment.sorted.bed -e GATC -o Harm.primary.scaffold -m...
This is causing various downstream issues, as the next logical step after running SALSA is to manually edit the assembly, and juicebox seems to be the only tool to do...
Dear developers, Thanks a lot for writing this super easy-to-use tool! I'm new in doing scaffolding with Hi-C data and also in using SALSA. I recently ran salsa with our...
hello, I'm trying to assemble a plant genome of roughly 4Gbp with 11 chromosomes. ATM I'm working on haploid assembly. I've got about 3000 contings using hifiasm, and SALSA produced...
Thanks again for making SALSA! I've been running it through the Docker container from Biocontainers, which autobuilds from the conda environment. This works very well for running SALSA itself, but...
Hi, I would like to report that Salsa still seems to sometimes run more iterations than stated in the call. More precisely, I requested the default number of iterations (3),...
I have loaded juicer_tools_1.22.01.jar to the JUICER_JAR variable like as following: JUICER_JAR=/mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/SALSA-master/juicer_tools_1.22.01.jar and i run the program like convert.sh scaffolds #here, scaffolds is the directory where the final fasta, agp...
Is duplicate marking necessary? I saw in the readme, it was recommended to run arima mapping pipeline. However, I had already ran juicer pipeline which does not run duplicates marking....
Hi, How to get a Python3 supported version of SALSA? Best, Kun
