Background The process of generating raw genome sequence data continues to become
cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished …

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome
data, but a lack of consensus about benchmarking complicates performance assessment. …

High-throughput sequencing data sets are usually deposited in public repositories (eg, the
European Nucleotide Archive) to ensure reproducibility. As the amount of data has reached …

Low-cost short read sequencing technology has revolutionized genomics, though it is only
just becoming practical for the high-quality de novo assembly of a novel large genome. We …

… (2010), we do a maximum-likelihood estimation of the parameters using the optim function
in R (BFGS algorithm). Let d be the number of distinct k-mers present in the histogram. Let …

Public databases contain a planetary collection of nucleic acid sequences, but their systematic
exploration has been inhibited by a lack of efficient methods for searching this corpus, …

… where r = m/n is the number of bits per element. For a fixed ratio r, minimizing Equation 1
yields the optimal number of hash functions h≈0.7r, for which F is approximately 0.6185 r . …

Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the
preliminary step of many bioinformatics applications. However, state of the art k-mer counting …

… An intermediate model was also considered by Chikhi et al. [2014], where S is parametrized
by the number of maximal unitigs … The type of index varies: The FM-index is used by Chikhi …

… parasitica ACP43 were incubated in RNAse R 1X reaction buffer, 1 U of RNAse R for 5,
15 or 30 minutes at 37 C. Negative controls were obtained mixing 2 µg of total RNA with the …