GSNAPGamma Soluble NSF Attachment Protein
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Reads were quality-filtered (requiring a quality score [greater than or equal to] 20 in at least 90% of nucleotides), adapters removed, and aligned with GSNAP software (Wu and Nacu 2010; Zhang et al.
Several programs are available for such analysis, including Qpalma, Splicemap, Mapsplice, TopHat, GSNAP and PALMapper, in which the TopHat algorithm pairs candidate exons and evaluates the alignment of reads to such candidates (Trapnell et al., 2009).
Furthermore, in this newest version of Sequencher, the BWA algorithm has joined a lineup comprising the alignment algorithms GSNAP and Maq, as well as the de novo assembly tool, Velvet.