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Background Some applications, especially those clinical applications requiring high accuracy of sequencing data, usually have to face the troubles caused by unavoidable sequencing errors. Several tools have been proposed to profile the sequencing quality, but few of them can quantify or correct the sequencing errors. This unmet requirement motivated us to develop AfterQC, a tool with functions to profile sequencing errors and correct most of them, plus highly automated quality control and data filtering features. Different from most tools, AfterQC analyses the overlapping of paired sequences for pair-end sequencing data. Based on overlapping analysis, AfterQC can detect and cut adapters, and furthermore it gives a novel function to correct wrong bases in the overlapping regions. Another new feature is to detect and visualise sequencing bubbles, which can be commonly found on the flowcell lanes and may raise sequencing errors. Besides normal per cycle quality and base content plotting, AfterQC also provides features like polyX (a long sub-sequence of a same base X) filtering, automatic trimming and K-MER based strand bias profiling. Results For each single or pair of FastQ files, AfterQC filters out bad reads, detects and eliminates sequencer’s bubble effects, trims reads at front and tail, detects the sequencing errors and corrects part of them, and finally outputs clean data and generates HTML reports with interactive figures. AfterQC can run in batch mode with multiprocess support, it can run with a single FastQ file, a single pair of FastQ files (for pair-end sequencing), or a folder for all included FastQ files to be processed automatically. Based on overlapping analysis, AfterQC can estimate the sequencing error rate and profile the error transform distribution. The results of our error profiling tests show that the error distribution is highly platform dependent. Conclusion Much more than just another new quality control (QC) tool, AfterQC is able to perform quality control, data filtering, error profiling and base correction automatically. Experimental results show that AfterQC can help to eliminate the sequencing errors for pair-end sequencing data to provide much cleaner outputs, and consequently help to reduce the false-positive variants, especially for the low-frequency somatic mutations. While providing rich configurable options, AfterQC can detect and set all the options automatically and require no argument in most cases.

Estimating the genomic location and length of identical-by-descent (IBD) segments among individuals is a crucial step in many genetic analyses. However, the exponential growth in the size of biobank and direct-to-consumer genetic data sets makes accurate IBD inference a significant computational challenge. Here we present the templated positional Burrows–Wheeler transform (TPBWT) to make fast IBD estimates robust to genotype and phasing errors. Using haplotype data simulated over pedigrees with realistic genotyping and phasing errors, we show that the TPBWT outperforms other state-of-the-art IBD inference algorithms in terms of speed and accuracy. For each phase-aware method, we explore the false positive and false negative rates of inferring IBD by segment length and characterize the types of error commonly found. Our results highlight the fragility of most phased IBD inference methods; the accuracy of IBD estimates can be highly sensitive to the quality of haplotype phasing. Additionally, we compare the performance of the TPBWT against a widely used phase-free IBD inference approach that is robust to phasing errors. We introduce both in-sample and out-of-sample TPBWT-based IBD inference algorithms and demonstrate their computational efficiency on massive-scale data sets with millions of samples. Furthermore, we describe the binary file format for TPBWT-compressed haplotypes that results in fast and efficient out-of-sample IBD computes against very large cohort panels. Finally, we demonstrate the utility of the TPBWT in a brief empirical analysis, exploring geographic patterns of haplotype sharing within Mexico. Hierarchical clustering of IBD shared across regions within Mexico reveals geographically structured haplotype sharing and a strong signal of isolation by distance. Our software implementation of the TPBWT is freely available for noncommercial use in the code repository (https://github.com/23andMe/phasedibd, last accessed January 11, 2021).

The term ‘bioturbation’ is frequently used to describe how living organisms affect the substratum in which they live. A closer look at the aquatic science literature reveals, however, an inconsistent usage of the term with increasing perplexity in recent years. Faunal disturbance has often been referred to as particle reworking, while water movement (if considered) is referred to as bioirrigation in many cases. For consistency, we therefore propose that, for contemporary aquatic scientific disciplines, faunal bioturbation in aquatic environments includesall transport processes carried out by animals that directly or indirectly affect sediment matrices. These processes include both particle reworking and burrow ventilation.With this definition, bioturbation acts as an ‘umbrella’ term that covers all transport processes and their physical effects on the substratum. Particle reworking occurs through burrow construction and maintenance, as well as ingestion and defecation, and causes biomixing of the substratum. Organic matter and microorganisms are thus displaced vertically and laterally within the sediment matrix. Particle reworking animals can be categorized as biodiffusors, upward conveyors, downward conveyors and regenerators depending on their behaviour, life style and feeding type. Burrow ventilation occurs when animals flush their open- or blind-ended burrows with overlying water for respiratory and feeding purposes, and it causes advective or diffusive bioirrigation ex change of solutes between the sediment pore water and the overlying water body. Many bioturbating species perform reworking and ventilation simultaneously. We also propose that the effects of bioturbation on other organisms and associated processes (e.g. microbial driven biogeochemical transformations) are considered within the conceptual framework of ecosystem engineering.

Macrobenthic invertebrates are widely distributed on sediments, and the micro‐morphology such as burrows and sand mounds due to their bioturbation activities can cause substantial changes in hyporheic exchange (HE). This study explores the characteristics of HE induced by benthic burrows through flume experiments and numerical simulations, focusing on the influence of burrow depth, mound height, and inter‐burrow distance. Our findings reveal that burrows enhance HE by forming preferential flow conduits. With the increased interfacial pressure drop and the newly formed circulations, the pore water tends to outflow through burrow sidewalls along the preferential paths in greater velocity under the enhanced advection, and the “pumping” effects persist even below the burrow depth. The pore water flux increased by 10.76 times on the burrow sidewall at most. Eddies are induced by mounds above the streambed, changing the inflow/outflow patterns on the interface. The interfacial exchange rate below eddies is decreased while the solute can inflow within more distant ranges away from burrows. The effects of mound height carry out in the shallow streambed, and quickly decrease as penetration depth increases. Variations in inter‐burrow distance affect the transition process of HE from advection‐ to dispersion‐dominated. As the distance increases, the solute transport is promoted first due to the enhanced advection, and then decreased with the weakened advection and the larger proportion of the dispersion. This study provides important insights into the key mechanism of HE, highlighting the critical role of benthic burrows in aquatic ecosystems. Plain Language Summary Benthic organisms, like clams and worms, dig burrows and pile up mounds on streambeds, breaking the original shapes of streambed interface, which can significantly affect water flow and solute transport in rivers. This study used indoor physical experiments and numerical simulations to understand these effects. We find that burrows, acting as conduits with “pumping” effect, are beneficial for water and solute movement between the streambed and the ground water, and deeper burrows can bring more significant impacts. Mounds make impacts by inducing eddies above the streambed, which influence the water inflow and outflow and further influence the solute transport. The distance between burrows can affect the main driving force for the exchange between surface water and groundwater, and there is an optimal distance that solute transport fastest in the streambed. We believe that benthic burrows can be used as a medium to connect the water ecological environment and the aquatic organisms, in order to better understand the natural material cycling and reaction processes. Key Points Burrows enhance hyporheic exchange (HE) by forming preferential flow conduits, and the influence persists even below the burrow depth Eddies induced by mounds alter the interfacial inflow/outflow pattern and affect HE significantly in the shallow streambed Variations in inter‐burrow distance affect the transition process of HE from advection‐ to dispersion‐dominated

Migrating mudbanks are characteristic features of the vast Amazon-Guianas coastline along Northeastern South America. As illustrated by sites in French Guiana, consolidating mudflats that periodically transition to mangrove forest are permeated by extensive crustacean burrow systems, sometimes in isolation but more often in close association with morpho-sedimentary structures such as tidal pools and channels. Burrow structures are critical to mangrove growth. In this study, we evaluated the ways in which burrows act as complex conduits that plumb deposits for solute exchange with overlying water. We sampled burrows during low tide when irrigation is inhibited and burrow water rapidly becomes anoxic. The products of diagenetic reactions, for example: NH4+, N2, and Si(OH)4, build up with time, revealing sedimentary reaction rates and fluxes. When oxygenated, burrow walls are zones of intense coupled redox reactions such as nitrification-denitrification. Build-up often is lower in burrows connected directly to tidal pools where photosynthetic activity consumes remineralized nutrients, and burrows can remain periodically irrigated at low tide. During flood, burrows, particularly those that connect tidal pools laterally to channels, can be rapidly flushed and oxygenated as channel water rises and then spreads across flats. Burrow flushing produces enhanced concentrations of nutrients within the leading edge of the flood as seawater moves progressively towards and into adjacent mangroves. Estimates of burrow volumes obtained from drone surveys together with burrow solute production rates allow upscaling of burrow-sourced metabolite fluxes; however, these are extremely variable due to variable burrow geometries, connections between burrows, pools, and channels, and burrow water residence times (oxygenation). The flushing of burrows during flood results in a rectification of sediment-water fluxes shoreward and enhances the delivery of nutrients from the flats into adjacent mangroves and pools, presumably stimulating colonization and forest growth.

Despite great general benefits derived from plastic use, accumulation of plastic material in ecosystems, and especially microplastic, is becoming an increasing environmental concern. Microplastic has been extensively studied in aquatic environments, with very few studies focusing on soils. We here tested the idea that microplastic particles (polyethylene beads) could be transported from the soil surface down the soil profile via earthworms. We used Lumbricus terrestris L., an anecic earthworm species, in a factorial greenhouse experiment with four different microplastic sizes. Presence of earthworms greatly increased the presence of microplastic particles at depth (we examined 3 soil layers, each 3.5 cm deep), with smaller PE microbeads having been transported downward to a greater extent. Our study clearly shows that earthworms can be significant transport agents of microplastics in soils, incorporating this material into soil, likely via casts, burrows (affecting soil hydraulics), egestion and adherence to the earthworm exterior. This movement has potential consequences for exposure of other soil biota to microplastics, for the residence times of microplastic at greater depth, and for the possible eventual arrival of microplastics in the groundwater.

Carcinoma cuniculatum (CC) is an uncommon variant of squamous cell carcinoma (SCC). It is a low-grade tumor with an endophytic and burrowing growth pattern. The lesion initially presents as a condyloma or a hyperkeratinized patch, which eventually ulcerates and features sinuses that discharge keratinous material. To date, CC remains rare, with about 75 reported cases, and it is frequently missed or misdiagnosed. The aim of the present work is to report five cases of CC in the gingivobuccal complex and highlight its main clinicopathological diagnostic features: an exophytic cobblestone surface and a characteristic endophytic burrowing architecture, as well as to differentiate it from other closely similar lesions, including verrucous carcinoma, papillary squamous cell carcinoma, and well-differentiated conventional oral squamous cell carcinoma. An accurate diagnosis of CC requires clinicians’ and pathologists’ awareness of this entity, a thorough understanding of the diagnostic clinical and histopathological evidence, and the ability to differentiate it from similar lesions.

Seven earthworm ecological categories, including anecics, endogeics and epigeics, were defined by Marcel Bouché in 1972 based only on morpho-anatomical characteristics measured on European lumbricids. These categories had an outstanding success, and their use was generalized even outside of Europe. However, most of the time, only the three main categories are used, and over two decades, these categories have been considered functional groups, i.e. to presume how earthworms influence the soil functioning. Moreover, this relationship between ecological categories and functional groups is seldom tested and often uncritically accepted by soil biology researchers. It is then not surprising to observe unexpected trends when earthworm species are gathered in ecological categories to, for instance, analyze burrow systems or cast properties. We believe it is time to acknowledge that ecological categories are not functional, because they were not made for this purpose. We also propose three future directions in order to either improve our knowledge on the functional effects of earthworms or to build new authentically functional groups: (i) going back to the seven initial ecological categories to provide greater accuracy than the usage of the simplified three-level classification; (ii) testing, for a set of selected species, the functionality of the groups, being ecological categories or new tailored ones; and (iii) using trait-based approach in order to study the correlation between some earthworm traits and main soil functions.