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only the best (genome assemblies) is a Hi-C / HiFi pipeline specifically designed for phasing
Checkout the wiki, and tutorial
In order to utilize this pipeline:
- singularity (https://sylabs.io/singularity/) must be installed
- nextflow (https://www.nextflow.io/) must be installed Most HPC support groups will either already have these tools installed, or be willing to install them as modules
otb operates from a local directory, and must be ran as ./otb.sh since it sources some shell scripts in the scr directory.
we recomend that you set NXF_SINGULARITY_LIBRARYDIR in your bashrc (or similar CLI) environment, otb containers will be stored at that location.
in order to use otb download this repository and use ./otb.sh, an example:
./otb.sh --runner sge --mode homozygous --threads 40 -f otb_test_file_R2.fastq -r otb_test_file_R1.fastq --polish-type simple --reads otb_test.bamotb runs in the following fashion:
otb is fully featured and utilzes the following softwares:
- bbtools
- genomescope2
- hifiasm
- jellyfish
- pbadapterfilt
- ragtag
- samtools
- shhquis
- busco
- hicstuff
- any2fasta
- blobtools
- merfin
- deep variant
- yahs
- bcftools
- bwa
- fcs-adaptor
otb now has a preprint. Preprint: https://doi.org/10.32942/X2T897
otb is in the public domain in the United States per 17 U.S.C. § 105