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q-bio.GN2013
Turtle: Identifying frequent k-mers with cache-efficient algorithms
Rajat Shuvro Roy, Debashish Bhattacharya, Alexander Schliep
Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing experiments. Infrequent k-mers are assumed to be a result o…
q-bio.GN2011
SLIQ: Simple Linear Inequalities for Efficient Contig Scaffolding
Rajat S. Roy, Kevin C. Chen, Anirvan M. Sengupta +1
Scaffolding is an important subproblem in "de novo" genome assembly in which mate pair data are used to construct a linear sequence of contigs separated by gaps. Here we present SL…