Seqnature: incorporate SNPs and Indels into a reference genome
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haplotype_files
README.md
adjust_annotations.py
adjust_individualized_annotations.py
build_individualized_genome.py
build_new_sequence_from_vcfs.py
changelog
do_DO.sh
reconstruct_NCBI.py
reference.py

README.md

#Seqnature

##Seqnature is replaced!

The Jackson Laboratory has released a new tool, g2gtools, with a superset of the features in the seqnature suite. Please use it instead.

Seqnature is no longer in maintenance.

The g2gtools are available at: https://github.com/churchill-lab/g2gtools.

##Citing

If you use Seqnature for your published research, please cite:

Munger SC, Raghupathy N, Choi KB, 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, In Press.