Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.
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ABSTRACT:
SUBMITTER: Fellows Yates JA
PROVIDER: S-EPMC7977378 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.ResultsHere we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants.ConclusionsEAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.
| S-EPMC4815194 | biostudies-literature
Project description:BackgroundCumulative sequencing efforts have yielded enough genomes to construct pangenomes for dozens of bacterial species and elucidate intraspecies gene conservation. Given the diversity of organisms for which this is achievable, similar analyses for ancestral species are feasible through the integration of pangenomics and phylogenetics, promising deeper insights into the nature of ancient life.ResultsWe construct pangenomes for 183 bacterial species from 54,085 genomes and identify their core genomes using a novel statistical model to estimate genome-specific error rates and underlying gene frequencies. The core genomes are then integrated into a phylogenetic tree to reconstruct the core genome of the last bacterial common ancestor (LBCA), yielding three main results: First, the gene content of modern and ancestral core genomes are diverse at the level of individual genes but are similarly distributed by functional category and share several poorly characterized genes. Second, the LBCA core genome is distinct from any individual modern core genome but has many fundamental biological systems intact, especially those involving translation machinery and biosynthetic pathways to all major nucleotides and amino acids. Third, despite this metabolic versatility, the LBCA core genome likely requires additional non-core genes for viability, based on comparisons with the minimal organism, JCVI-Syn3A.ConclusionsThese results suggest that many cellular systems commonly conserved in modern bacteria were not just present in ancient bacteria but were nearly immutable with respect to short-term intraspecies variation. Extending this analysis to other domains of life will likely provide similar insights into more distant ancestral species.
| S-EPMC10411014 | biostudies-literature
Project description:Compi is an application framework to develop end-user, pipeline-based applications with a primary emphasis on: (i) user interface generation, by automatically generating a command-line interface based on the pipeline specific parameter definitions; (ii) application packaging, with compi-dk, which is a version-control-friendly tool to package the pipeline application and its dependencies into a Docker image; and (iii) application distribution provided through a public repository of Compi pipelines, named Compi Hub, which allows users to discover, browse and reuse them easily. By addressing these three aspects, Compi goes beyond traditional workflow engines, having been specially designed for researchers who want to take advantage of common workflow engine features (such as automatic job scheduling or logging, among others) while keeping the simplicity and readability of shell scripts without the need to learn a new programming language. Here we discuss the design of various pipelines developed with Compi to describe its main functionalities, as well as to highlight the similarities and differences with similar tools that are available. An open-source distribution under the Apache 2.0 License is available from GitHub (available at https://github.com/sing-group/compi). Documentation and installers are available from https://www.sing-group.org/compi. A specific repository for Compi pipelines is available from Compi Hub (available at https://www.sing-group.org/compihub.
| S-EPMC8237318 | biostudies-literature
Project description:Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool's inputs, outputs, and other execution details. CWL documents can include instructions for executing tools inside software containers. Accordingly, CWL tools are portable-they can be executed on diverse computers-including personal workstations, high-performance clusters, or the cloud. CWL also supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used primarily for batch processing of large datasets, especially in genomics. But it can also be used for analytical steps of a study. This article explains key concepts about CWL and software containers and provides examples for using CWL in biology research. CWL documents are text-based, so they can be created manually, without computer programming. However, ensuring that these documents conform to the CWL specification may prevent some users from adopting it. To address this gap, we created ToolJig, a Web application that enables researchers to create CWL documents interactively. ToolJig validates information provided by the user to ensure it is complete and valid. After creating a CWL tool or workflow, the user can create 'input-object' files, which store values for a particular invocation of a tool or workflow. In addition, ToolJig provides examples of how to execute the tool or workflow via a workflow engine. ToolJig and our examples are available at https://github.com/srp33/ToolJig.
| S-EPMC8514239 | biostudies-literature
Project description:Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities-together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches. Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity. Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.
| S-EPMC6049006 | biostudies-literature
Project description:BackgroundWe propose the computational reconstruction of a whole bacterial ancestral genome at the nucleotide scale, and its validation by a sequence of ancient DNA. This rare possibility is offered by an ancient sequence of the late middle ages plague agent. It has been hypothesized to be ancestral to extant Yersinia pestis strains based on the pattern of nucleotide substitutions. But the dynamics of indels, duplications, insertion sequences and rearrangements has impacted all genomes much more than the substitution process, which makes the ancestral reconstruction task challenging.ResultsWe use a set of gene families from 13 Yersinia species, construct reconciled phylogenies for all of them, and determine gene orders in ancestral species. Gene trees integrate information from the sequence, the species tree and gene order. We reconstruct ancestral sequences for ancestral genic and intergenic regions, providing nearly a complete genome sequence for the ancestor, containing a chromosome and three plasmids.ConclusionThe comparison of the ancestral and ancient sequences provides a unique opportunity to assess the quality of ancestral genome reconstruction methods. But the quality of the sequencing and assembly of the ancient sequence can also be questioned by this comparison.
| S-EPMC4603589 | biostudies-literature
Project description:Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.
| S-EPMC10055538 | biostudies-literature
Project description:Abstract Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next?generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole?genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA. Our method for ancient DNA mapping and filtering contamination can decrease the contamination to very low level. We believe that the work we present can facilitate future studies of ancient DNA.
| S-EPMC7790629 | biostudies-literature
Project description:One of the extraordinary characteristics of the biological brain is the low energy expense it requires to implement a variety of biological functions and intelligence as compared to the modern artificial intelligence (AI). Spike-based energy-efficient temporal codes have long been suggested as a contributor for the brain to run on low energy expense. Despite this code having been largely reported in the sensory cortex, whether this code can be implemented in other brain areas to serve broader functions and how it evolves throughout learning have remained unaddressed. In this study, we designed a novel brain-machine interface (BMI) paradigm. Two macaques could volitionally generate reproducible energy-efficient temporal patterns in the primary motor cortex (M1) by learning the BMI paradigm. Moreover, most neurons that were not directly assigned to control the BMI did not boost their excitability, and they demonstrated an overall energy-efficient manner in performing the task. Over the course of learning, we found that the firing rates and temporal precision of selected neurons co-evolved to generate the energy-efficient temporal patterns, suggesting that a cohesive rather than dissociable processing underlies the refinement of energy-efficient temporal patterns.
| S-EPMC9599309 | biostudies-literature
Project description:Millimetre-wave imaging is a powerful non-destructive inspection technique which has become widely used in areas such as through-the-wall imaging or concealed weapon detection. Nevertheless, current systems are usually limited to either a single view point providing a limited 3D millimeter-wave model or a multiview relying on the accurate movement of a robot arm through precise positions resulting in very bulky systems. In this paper, we present a set of techniques to achieve a multiview millimetre-wave scanner. The aperture of the scanner is kept below 16 cm so it can be portable and, consequently, multiview can be achieved by simple hand movements. In addition, optical images are also acquired with a two-fold purpose: i) building a complementary 3D-model by employing Structure from Movement (SfM) techniques; ii) estimating the scanner position and poses. The proposed technology is illustrated for people screening, proving the capacity of the system to detect hidden weapons.
| S-EPMC5527015 | biostudies-literature