SHRiMP2: Sensitive yet Practical Short Read Mapping

By Matei David, Misko Dzamba, Dan Lister, Lucian Ilie, Michael Brudno. Bioinform., 2011

387 citations recorded by the source corpus.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA (2015, methodology): “Additionally, we show that using a sensitive aligner like SHRIMP [25] does not cause drops in coverage around regions of high divergence of the Denisovan mitochondrial genome to the human mtDNA, thus allowing for a more reliable contamination estimate (see Additional file 1: Results, Section 2.1).”
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping (2013, methodology): “The hash-based aligners, Eland (AJ Cox, Illumina, San Diego), MAQ (Li et al. 2008), mrFAST/mrsFast (Alkan et al. 2009; Hach et al. 2010), SHRiMP (Rumble et al. 2009; David et al. t2011), and ZOOM (Lin et al. 2008; Zhang et al. 2010) hash the reads and fit these hashes to the reference genome, while ”