Sequencing DNA with nanopores: Troubles and biases

Oxford Nanopore Technologies’ (ONT) long read sequencers offer access to longer DNA fragments than previous sequencer generations, at the cost of a higher error rate. While many papers have studied read correction methods, few have addressed the detailed characterization of observed errors, a task complicated by frequent changes in chemistry and software in ONT technology. The MinION sequencer is now more stable and this paper proposes an up-to-date view of its error landscape, using the most mature flowcell and basecaller. We studied Nanopore sequencing error biases on both bacterial and human DNA reads. We found that, although Nanopore sequencing is expected not to suffer from GC bias, it is a crucial parameter with respect to errors. In particular, low-GC reads have fewer errors than high-GC reads (about 6% and 8% respectively). The error profile for homopolymeric regions or regions with short repeats, the source of about half of all sequencing errors, also depends on the GC rate and mainly shows deletions, although there are some reads with long insertions. Another interesting finding is that the quality measure, although over-estimated, offers valuable information to predict the error rate as well as the abundance of reads. We supplemented this study with an analysis of a rapeseed RNA read set and shown a higher level of errors with a higher level of deletion in these data. Finally, we have implemented an open source pipeline for long-term monitoring of the error profile, which enables users to easily compute various analysis presented in this work, including for future developments of the sequencing device. Overall, we hope this work will provide a basis for the design of better error-correction methods.

Error propagation dynamics of velocimetry-based pressure field calculations (2): on the error profile

This work investigates the propagation of error in a Velocimetry-based Pressure field reconstruction (VPressure) problem to determine and explain the effects of error profile of the data on the error propagation. The results discussed are an extension to those found in Pan et al. (2016). We first show how to determine the upper bound of the error in the pressure field, and that this worst scenario for error in the data field is unique and depends on the characteristics of the domain. We then show that the error propagation for a V-Pressure problem is analogous to elastic deformation in, for example, a Euler-Bernoulli beam or Kirchhoff-Love plate for one- and two-dimensional problems, respectively. Finally, we discuss the difference in error propagation near Dirichlet and Neumann boundary conditions, and explain the behavior using Green’s function and the solid mechanics analogy. The methods discussed in this paper will benefit the community in two ways: i) to give experimentalists intuitive and quantitative insights to design tests that minimize error propagation for a V-pressure problem, and ii) to create tests with significant error propagation for the benchmarking of V-Pressure solvers or algorithms. This paper is intended as a summary of recent research conducted by the authors, whereas the full work has been recently published (Faiella et al., 2021).

Effectiveness of frequent inventory audits in retail stores: an empirical evaluation

Purpose The purpose of this paper is to focus on the effectiveness of the inventory audit process to manage operational issues related to inventory errors in retail stores. An evaluation framework is proposed based on developing an error profile of store inventory using product attributes and inventory information. Design/methodology/approach A store inventory error profile is developed using data on price, sales, popularity, replenishment cycle, inventory levels and inventory errors. A simulation model of store inventory management system grounded in empirical data is used to evaluate the effectiveness of the inventory audit process in a high SKU-variety retail store. The framework is tested using a large transaction data set comprised of over 200,000 records for 7,400 SKUs. Findings The results show that store inventory exhibits different inventory error profile groups that would determine the effectiveness of store inventory audits. The results also identify an interaction effect between store inventory policies and replenishment process that moderates the effectiveness of inventory audits. Research limitations/implications The analysis is based on data collected from a single focal firm and does not cover all the different segments of the retail industry. However, the evaluation framework presented in the paper is fully generalizable to different retail settings offering opportunity for additional studies. Practical implications The findings about the role of different error profile groups and the interaction effect of store audits with inventory and store replenishments would help retailers incorporate a more effective inventory audit process in their stores. Originality/value This paper presents a novel approach that uses store inventory profiles to evaluate the effectiveness of inventory audits. Unlike previous papers, it is the first empirical study in this area that is based on inventory error data gathered from multiple audits that identify the interaction effect of inventory policy and replenishments on the inventory audit process.

PROFIL KESALAHAN MAHASISWA PADA MATA KULIAH ANALISIS KOMPLEKS

This research is used to analyze the error profile encountered by STKIP PGRI Pacitan students in the course of Complex Analysis on the subject of PolarShape. The type of research used is qualitative descriptive. Subjects used as many as 2 students. Data collection methods used are test methods andinterview methods. The results of this study are on Misunderstanding, Transformation Errors and Process Errors. Misunderstanding is to assume thesymbol R = r when R ≠ r. Then assume that in calculating the root of the value of negative/positive just the same, even though the end result also remains the same. And it is often reversed between the values of x and y. Transformation error is inverted in determining x and y for cos arc formula. While the Process Error is unable to determine the magnitude of a special angle adjusted to the location of the point of z. weak in calculating the powers in the form of fractions. And wrong in drawing the z-point coordinates.