Reconstruction algorithms for DNA-storage systems.

Motivated by DNA storage systems, this work presents the DNA reconstruction problem, in which a length-n string, is passing through the DNA-storage channel, which introduces deletion, insertion and substitution errors. This channel generates multiple noisy copies of the transmitted string which are called traces. A DNA reconstruction algorithm is a mapping which receives t traces as an input and produces an estimation of the original string. The goal in the DNA reconstruction problem is to minimize the edit distance between the original string and the algorithm's estimation. In this work, we present several new algorithms for this problem. Our algorithms look globally on the entire sequence of the traces and use dynamic programming algorithms, which are used for the shortest common supersequence and the longest common subsequence problems, in order to decode the original string. Our algorithms do not require any limitations on the input and the number of traces, and more than that, they perform well even for error probabilities as high as 0.27. The algorithms have been tested on simulated data, on data from previous DNA storage experiments, and on a new synthesized dataset, and are shown to outperform previous algorithms in reconstruction accuracy.

SOLQC: Synthetic Oligo Library Quality Control tool.

MOTIVATION: Recent years have seen a growing number and an expanding scope of studies using synthetic oligo libraries for a range of applications in synthetic biology. As experiments are growing by numbers and complexity, analysis tools can facilitate quality control and support better assessment and inference. RESULTS: We present a novel analysis tool, called SOLQC, which enables fast and comprehensive analysis of synthetic oligo libraries, based on NGS analysis performed by the user. SOLQC provides statistical information such as the distribution of variant representation, different error rates and their dependence on sequence or library properties. SOLQC produces graphical reports from the analysis, in a flexible format. We demonstrate SOLQC by analyzing literature libraries. We also discuss the potential benefits and relevance of the different components of the analysis. AVAILABILITY AND IMPLEMENTATION: SOLQC is a free software for non-commercial use, available at https://app.gitbook.com/@yoav-orlev/s/solqc/. For commercial use please contact the authors. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Sources and evolution of anthropogenic lead in dated sediments from Lake Clair, Québec, Canada.

Two sediments cores were collected from the deepest part of Lake Clair (Québec, Canada) to assess the historical sources of Pb additions to the lake. The cores were collected by divers by carefully inserting a Plexiglas tube into the sediments. To determine the stratigraphic ages of the sediments, (210)Pb and (137)Cs activities were counted by gamma-ray spectroscopy. Lead concentrations and isotopic ratios were performed by inductively coupled plasma-mass spectrometry (ICP-MS), following digestion of the samples with a mixture of HF, HNO(3), and HClO(4) acids and Pb separation by anion-exchange chromatography. Starting at the middle of the 19th century, Pb content of the sediments increased until 1975. The maximum Pb enrichment factor of 35 times (relative to the natural background) was found in sediments deposited in 1975. At this time, excess Pb flux was estimated to be about 0.03 g m(-2) yr(-1). Before 1872, the Pb isotopic ratios were relatively stable (mean (206)Pb/(207)Pb = 1.20 +/- 0.01), reflecting the natural Pb background. Between 1872 and 1894, the source of anthropogenic Pb was highly radiogenic as shown by the Pb isotopic signatures of the sediments (mean (206)Pb/(207)Pb = 1.22 +/- 0.01), possibly reflecting deforestation and agricultural developments in the St.-Lawrence Valley. Between 1894 and 1937, widespread use of industrial and domestic charcoals may explain the isotopic composition of Pb accumulated in the sediments (mean (206)Pb/(207)Pb = 1.19 +/- 0.01). From 1937 to 1975, Pb isotopic compositions became less radiogenic ((206)Pb/(207)Pb from 1.18 to 1.17) even though elemental Pb abundance reached extremely high values (623 mg kg(-1)). This isotopic shift reflects increased use of alkyl-lead in gasoline. For sediments accumulated between 1967 and 1996, the U.S. contribution to anthropogenic Pb accumulated in Lake Clair sediments amounted to between 30 and 63%.