Software

HPV integration point detection tool for targeted capture sequencing data

Source code and documentation is 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

Pre-mAsking Long reads for Mobile Element inseRtion

Source code and documentation is 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

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

Source code and documentation is 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.

Analysis and validation of structural variation from long read sequencing data

Source code and documentation is 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

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

Source code and documentation is 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

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

Source code and documentation is 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

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 is 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

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 is 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