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Seqnature specifications


Unique identifier OMICS_05840
Name Seqnature
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Gary Churchill <>

Publication for Seqnature

Seqnature in pipelines

PMCID: 5524189
PMID: 27270587
DOI: 10.1038/nm.4115

[…] samples are archived at geo under the accession numbers gse45684 and gse80162, respectively. individualized genome and transcriptome sequences were constructed for every do and strain sample using seqnature software. rna-seq reads were aligned to their respective individualized transcriptome using the bowtie aligner, and gene expression was quantified from the read alignment profiles using […]

PMCID: 4287450
PMID: 25568937
DOI: 10.1371/journal.pgen.1004916

[…] highly divergent with over 17 million snps and 2.5 million indels. to reduce alignment bias in haplotype-specific estimates from the genetic variations, we created subspecies-specific genomes using seqnature , by incorporating known snps and indels . we then created selective diploid genomes; for example for bxc f1 hybrids we would create one for b6 haplotype and one for cast haplotype, […]

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Seqnature in publications

PMCID: 5636166
PMID: 28961251
DOI: 10.1371/journal.pgen.1007025

[…] chromosome are more accurately mapped than reads from an a/j-derived chromosome []. to avoid potential mapping biases, we created an “individualized genome” of the a/j mouse strain using the program seqnature [] with variant calls from the mouse genomes project that were downloaded from the sanger institute []. reads that were not mapped to the b6 genome were then mapped to the individualized aj […]

PMCID: 5266220
PMID: 28121987
DOI: 10.1371/journal.pgen.1006498

[…] mouse project[], files mgp.v3.snps.rsiddbsnpv137.vcf and mgp.v3.indels.rsiddbsnpv137.vcf, both on grcm38) to construct a d2 genome and the corresponding gene annotation file using the software seqnature[] (version 1.2). reads were aligned using tophat[] (tophat2 version 2.0.11, bowtie version, and samtools version, considering either the b6 genome (grcm38) or the d2 […]

PMCID: 5404925
PMID: 28438259
DOI: 10.7554/eLife.21476.035

[…] and produced 100-nucleotide-long reads., sequencing data were aligned with star 2.3 () to the grcm38 mouse reference genome (b6) or to pseudo-genomes created for the different strains using seqnature () to impute the high-quality variants reported by the mouse genomes project, release v3 ( the parameters used for mapping […]

PMCID: 5110614
PMID: 27651241
DOI: 10.1007/s00335-016-9663-6

[…] high-quality variants were then compared to ensembl reference annotations to identify those that occurred within genes. individual ils and iss genome and gene annotation files were generated using seqnature (v 1.0; munger et al. ) incorporating the most high-confidence set of snps and small indels for each strain into the mm10 reference (common and strain-distinct)., large structural […]

PMCID: 4687867
PMID: 26695660
DOI: 10.1371/journal.pone.0145176

[…] et al. [], which classifies reads as “graft”, “host”, “both”, “neither” or “ambiguous”. we used the non-obese diabetic (nod) genome sequences as the host reference genome (, where nod is the background strain of the scid strain, nod.cb17-prkdcscid/j, used in the engrafting. using this host reference genome rather than the mouse reference genome (mm10) […]

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Seqnature institution(s)
Supported by The Jackson Laboratory and National Institutes of Health (NIH) grants under awards P50GM076468; DK091207, DK66369, and DK58037; and F32HD074299.

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