INTRODUCTION Many genome projects were underway before the advent of high-throughput sequencing and have thus been supported by a wealth of genome information from other technologies. Such information frequently takes the form of linkage and physical maps, both of which can provide a substantial amount of data useful in de novo sequencing projects. Furthermore, the recent abundance of genome re...

MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 99.6 h on a single computing node with and without a graphics processing unit, respectively. MEGAHIT assembles the data as a whole, i.e. no pre-processing like partitioning and normalization was n...

Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 ...

We report here the draft genome sequence of a novel UV-resistant bacterium isolated from dry soil on the south coast of Puerto Rico. Based on polyphasic taxonomy, strain MC1A represents a new species and the name Solirubrum puertoriconensis is proposed. Assembly was performed using NGEN Assembler into eight contigs (N50 = 1,292,788), the largest of which included 1,549,887 bp. The draft genome ...

Our aim in this paper is twofold. First, to find the necessary and sufficient conditions to be satisfied by a given sequence of real numbers $vn%n50 ` to represent the ‘‘entropic moments’’ * [0,a]@r(x)# dx of an unknown non-negative, decreasing and differentiable ~a.e.! density function r(x) with a finite interval support. These moments are called entropic moments because they are closely conne...

BACKGROUND The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders, and used the genomes to construct a genome-scale avi...

Many studies have found a negative relationship between oil abundance and democracy. However, recent tried to upend this correlation by employing time-series techniques or finding conditionality on other factors. This study contributes the literature an Arellano Bond model that corrects for fixed effects adopts new variables from empirical studies. Comparing Eurasia Latin America 1960s 2010, we...

Motivation: Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50. Results: We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. We implemented the assessment proc...

~assuming the simulation box is cubic!, where qi and ri are the charge and position of particle i, L is the size of the simulation box, n5(n1 ,n2 ,n3), and the prime indicates that the i5 j terms are omitted when n50. The Ewald summation method has been widely used to handle the lattice sum in Eq. ~1!. In the method, the above-mentioned conditionally convergent series is written as a sum of a c...

MOTIVATION Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50. RESULTS We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. We implemented the assessment proc...