sharupaul/otb

Only The Best (Genome Assembly Tools)

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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.bam

otb 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