Pre-mAsking Long reads for Mobile Element inseRtion
Source code and documentation is available at https://github.com/mills-lab/PALMER.
Manuscript in preparation
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.
Sherman MD, Mills RE. BAMnostic- an OS-agnostic toolkit for genomic sequence analysis. Journal of Open Source Software, 3(28), 826.
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.
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.
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/.
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/.
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