Software

DiamondsDenovo: The goal of this tool is to find “diamonds in the rough” in the genome. It is used to identify regions of the genome with an excess of de novo variants. Available at https://github.com/TNTurnerLab/DiamondsDenovo.

Relevant Preprint: https://www.medrxiv.org/content/10.1101/2025.03.28.25324850v1

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CNPI: Copy Number Private Investigator, CNPI, is a copy number analysis toolkit developed for rapid analyses of copy number in the human genome. Available at https://github.com/TNTurnerLab/CNPI.

3D-CLUMP: 3D-CLustering by Mutation Position (3D-CLUMP) is an unsupervised clustering of amino acid residue positions where variants occur, without any prior knowledge of their functional importance, in 3D space. Available at https://github.com/tnturnerLab/3d-clump.

Relevant Publication: https://www.cell.com/cell-genomics/fulltext/S2666-979X%2825%2900063-1

acorn: An R package that works with de novo variants (DNVs) already called using a DNV caller (e.g., HAT). The toolkit is useful for extracting different types of DNVs and summarizing characteristics of the DNVs. Available at https://github.com/TNTurnerLab/acorn.

Relevant Publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05457-z

PYRUS: A tool for plotting copy number estimate data, from an individual, for user-specified regions of the genome. It has several options including plotting other individuals in the same region, plotting an annotation track, and writing out specific regions where the individuals have a copy number below or above given values. The input to the tool is bgzipped and tabix indexed bed files, which enables rapid plotting of the data. Available at https://github.com/TNTurnerLab/PYRUS.

Short Writeup: https://github.com/TNTurnerLab/PYRUS/blob/main/paper/paper.md

HAT: Hare And Tortoise, HAT, are two de novo variant callers we developed for parent-child trio sequencing data. Hare, as seen in Ng et al. 2022, uses the software Parabricks, v4.0.0-1, by NVIDIA, that leverages GPUs to accelerate variant calling, specifically for Haplotyecaller GATK 4.2.0 and DeepVariant v1.4.0. Tortoise uses freely available, open-source versions of these variant callers. We then use GLnexus to form family level joint-genotyped files to be run through our custom de novo variant filter. Available at https://github.com/TNTurnerLab/hat

Relevant Publications:
https://pubmed.ncbi.nlm.nih.gov/36054329/
https://pubmed.ncbi.nlm.nih.gov/38175776/

ACES: A workflow to query small sequences in a large set of genomes. It provides several outputs including BLAST results, a multiple sequence alignment file, a graphical fragment assembly file, and a phylogenetic tree file. Available at https://github.com/TNTurnerLab/ACES.

Relevant publication: https://pubmed.ncbi.nlm.nih.gov/34601580/

fitDNM for noncoding: fitDNM was originally developed by the Allen lab (http://people.duke.edu/~asallen/Software.html) in Jiang et al 2015, Am. J. Hum. Genet. (https://www.cell.com/ajhg/fulltext/S0002-9297(15)00277-3) to incorporate functional information in test of excess de novo mutational load. We adapted the pipeline, in collaboration with the Allen lab, to utilize CADD scores instead of PolyPhen-2 scores in order to run in noncoding regions of the genome and implemented a scalable version of the pipeline to test many elements at once. Given a bed file that contains the regions of interest one wants to test for a significant excess of de novo mutations and the corresponding variants to use, this pipeline will output two summary files that contain the p values and scores calculated by fitDNM for each element in the bed file in the “.fitDNM.report” file and a summary of all mutations found in these genomic regions in the “.mutation.report” file. Available at https://github.com/TNTurnerLab/fitDNM.

Relevant Publication: https://pubmed.ncbi.nlm.nih.gov/34256850/