Seqnature is a tool for building individualized genomes for inbred strains and heterogeneous outbred animals from characterized variant data (e.g. SNPs, indels) and haplotype information.
Seqnature software is available for download at https://github.com/jaxcs/Seqnature. Comprehensive usage information and examples are included at this link.
Seqnature was used to build imputed genomes and gene annotation files for the Collaborative Cross (CC) / Diversity Outbred (DO) founder strains from Sanger SNP and indel data (Release #20111102, ftp://ftp-mouse.sanger.ac.uk). Only high confidence SNPs (calls with ATG=1) and indels of less than 100 bases were included in this initial iteration. We will seek to accommodate more complex structural variants (e.g. inversions, translocations) in a future release of Seqnature.
The NCBIM37 genome was used as the reference, and gene annotations were based on Ensembl v67. Feature coordinates in the strain-specific annotation (.gtf) files were adjusted to reflect indels in the strain genome.
Munger SC, Raghupathy N, Choi K, Simons AK, Gatti DM, Hinerfeld DA, Svenson KL, Keller MP, Attie AD, Hibbs MA, Graber JH, Chesler EJ, and Churchill GA.
RNA-seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations
Genetics. 2014;198(1):59-73. PMCID: PMC4174954 [ Full Text ]