A Nextflow workflow encapsulating the computational components to take output from the 15:1 molar libraries of gDNA:cDNA sequenced on the PacBio Revio following the protocols published in "Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition".
Vollger MR, Korlach J, Eldred KC, Swanson E, Underwood JG, Cheng YH, Ranchalis J, Mao Y, Blue EE, Schwarze U, Munson KM, Saunders CT, Wenger AM, Allworth A, Chanprasert S, Duerden BL, Glass I, Horike-Pyne M, Kim M, Leppig KA, McLaughlin IJ, Ogawa J, Rosenthal EA, Sheppeard S, Sherman SM, Strohbehn S, Yuen AL; University of Washington Center for Mendelian Genomics (UW-CMG), Undiagnosed Diseases Network (UDN); Reh TA, Byers PH, Bamshad MJ, Hisama FM, Jarvik GP, Sancak Y, Dipple KM, Stergachis AB. Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition. bioRxiv [Preprint]. 2023 Sep 27:2023.09.26.559521. doi: 10.1101/2023.09.26.559521. PMID: 37808736; PMCID: PMC10557686.
There will be a final overarching single workflow but to develop the pieces and parts we need several steps to fully realize the system: Each of these will have a specific nextflow workflow to test out the steps.
pbsv assumes that the reads have been aligned to a reference, so we require pbmm2.
- pbmm2 containerized in pbmm2-docker using pbmm2
- pbsv containerized in pbsv-docker using pbsv
- k-mer-variant-phasing containerized in k-mer-variant-phasing-docker using k-mer-variant-phasing
- HiPhase containerzied in hiphase-docker using HiPhase
- hifiasm containerized in hifiasm-docker using hifiasm
- yak containerized in yak-docker using yak
- pb-CpG-tools containerized in pb-CpG-tools-docker using pb-CpG-tools
- pbfusion containerized in pbfusion-docker using pbfusion
- fiberseq-fire containerized in fiberseq-fire-docker using fiberseq-fire
Using the philosophy - is always an elements of style approach.
Input - process - output
Containerization at each of the process levels, ensures modular testing. Each of the processes in this workflow are made into Docker containers. GitHub Actions are used to Build Docker Images using the default parameters from the GitHub Workflows.
THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY SCIENCE and TECHNOLOGY CONSULTING LLC.