Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.
By Gerton A. Lunter, Martin Goodson. Genome Research, 2011
1,206 citations recorded by the source corpus.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/bc5265fc16bcd8211f2695ad9f840c1b62fb96b6
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In Molecular Biology
- Todd J. Treangen
- Steven L. Salzberg
- Heng Li
- Fritz J. Sedlazeck
- B. Faircloth
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- P. S. Ward
- M. Branstetter
Citations in the corpus
- NextGenMap: fast and accurate read mapping in highly polymorphic genomes (2013, methodology): “As hash-based representative we selected Stampy (Lunter and Goodson, 2011).”
- Identifying conserved genomic elements and designing universal bait sets to enrich them (2017, methodology): “2; triCas1 hereafter) using stampy (Lunter & Goodson 2011) with a substitution rate of 0 05 and streaming the resulting SAM alignment data to BAM format using samtools (Li et al. 2009).”
- Genome-wide evidence for speciation with gene flow in Heliconius butterflies (2013, neutral): “0.13 (Lunter and Goodson 2011).”
- Special features of RAD Sequencing data: implications for genotyping (2012, methodology): “…using standard tools designed for whole genome sequencing data (Nielsen et al. 2011), including aligners such as BWA (Li & Durbin 2009) and Stampy (Lunter & Goodson 2011), and genotypers such as those built into the Genome Analysis Tool Kit (GATK; DePr-isto et al. 2011) and SAMtools (Li 2011).”
- Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species (2012, neutral): “Polymorphism Discovery and Genotyping without a Reference Genome Due to short read lengths and high error rates, methods for analyzing second-generation sequencing data generally require mapping sequencing reads to a fully sequenced genome from the same or a very closely related species (divergence ”
- Computational methods for transcriptome annotation and quantification using RNA-seq (2011, background): “Seed methods 31–38 such as mapping and assembly with quality (MAQ) 33 and Stampy 35 find matches for short subsequences, termed ‘seeds’, assuming that at least each approach and their application to RNA-seq analysis.”