Software

• SearcHPV

  HPV integration point detection tool for targeted capture sequencing data

  Source code and documentation available at https://github.com/mills-lab/SearcHPV

  Reference: Pinatti LM, Gu W, Wang Y, El Hossiny A, Bhangale AD, Brummel CV, Carey TE, Mills RE, Brenner JC. SearcHPV, a novel approach to identify and assemble human papillomavirus-host genomic integration events in cancer. Cancer, in press

• palmer

  Pre-mAsking Long reads for Mobile Element inseRtion

  Source code and documentation available at https://github.com/mills-lab/PALMER

  Reference: Zhou W, Emery SB, Flasch DA, Wang Y, Kwan KY, Kidd JM, Moran JV, Mills RE. Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. Nucleic Acids Res. 2020 Feb 20;48(3):1146-1163

• bamnostic

  A pure Python multi-version tolerant, runtime and OS-agnostic BAM file parser and random access tool.

  Source code and documentation available at https://github.com/mills-lab/bamnostic

  Reference: Sherman MD, Mills RE. BAMnostic- an OS-agnostic toolkit for genomic sequence analysis. Journal of Open Source Software, 3(28), 826.

• VaPoR

  Analysis and validation of structural variation from long read sequencing data

  Source code and documentation available at https://github.com/mills-lab/vapor

  Reference: Zhao X, Weber AM, Mills RE. A recurrence-based approach for validating structural variation using long-read sequencing technology. GigaScience. 2017;6(8):1-9

• spectre

  This software is designed to identify regions of active translation from ribsome profiling sequence data.

  Source code and documentation available at https://github.com/mills-lab/spectre

  Reference: Chun SY, Rodriguez CM, Todd PK, Mills RE. SPECtre- a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data. BMC Bioinformatics 2016 Nov 25, 17(1), 482

• svelter

  This software is designed to identify both simple and complex rearrangements from paired-end sequencing data.

  Source code and documentation available at https://github.com/mills-lab/svelter

  Reference: Zhao X, Emery SB, Myers B, Kidd JM, Mills RE. Resolving complex structural genomic rearrangements using a randomized approach. Genome Biol 2016, 17(1), 126

• dinumt

  This software is designed to identify and genotype nuclear insertions of mitochondrial origin from whole genome sequence data. It consists of two programs, diumt (di-nu-mite), which identifies sites of insertions in a single sample and gnomit (geno-mite), which genotypes those sites across multiple samples.

  Source code and documentation available at https://github.com/mills-lab/dinumt/

  Reference: Dayama G, Emery SB, Kidd JM, Mills RE. The genomic landscape of polymorphic human nuclear mitochondrial insertions. Nucleic Acids Res 2014 Nov 10, 42(20), 12640-9

• canny

  This software was used to analyze 2,135 Agilent 1M CGH arrays designed to assess copy number variation genotypes in Phase 3 samples from the 1000 Genomes Project.

  Source code and documentation available at https://github.com/mills-lab/canny/

  Reference: Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A et al. An integrated map of structural variation in 2,504 human genomes. Nature 2015 Oct 1, 526(7571), 75-81