Related papers: Mapache: a flexible pipeline to map ancient DNA
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
The emergence of R, a freely available data analysis environment, brought to the researcher in any science field a set of well-concerted instruments of immense power and low cost. In botany and zoology, these instruments could be used, for…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
We developed pgMAP, an analysis pipeline to map gRNA sequencing reads from dual-targeting CRISPR screens. pgMAP output includes a dual gRNA read counts table and quality control metrics including the proportion of correctly-paired reads and…
Background. Life science is increasingly driven by Big Data analytics, and the MapReduce programming model has been proven successful for data-intensive analyses. However, current MapReduce frameworks offer poor support for reusing existing…
While Multimodal Large Language Models have achieved human-like performance on many visual and textual reasoning tasks, their proficiency in fine-grained spatial understanding, such as route tracing on maps remains limited. Unlike humans,…
The rapid development of the DNA nanotechnology field has been facilitated by advances in CAD software. However, as more complex concepts arose, the lag between the needs and software capabilities appeared. Further derailed by manual…
Scientific workflows automate the analysis of large-scale scientific data, fostering the reuse of data processing operators as well as the reproducibility and traceability of analysis results. In exploratory research, however, workflows are…
Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to millions of bases in a single read), and the option to…
We introduce \emph{ReMatching}, a novel shape correspondence solution based on the functional maps framework. Our method, by exploiting a new and appropriate \emph{re}-meshing paradigm, can target shape-\emph{matching} tasks even on meshes…
Analysis pipelines commonly use high-level technologies that are popular when created, but are unlikely to be readable, executable, or sustainable in the long term. A set of criteria is introduced to address this problem: Completeness (no…
Optimizing parallel programs for distributed systems is a complex task, often requiring significant code modifications. Task-based programming systems improve modularity by separating performance decisions from application logic, but their…
With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for…
The marine environment is one of the most important sources for microbial biodiversity on the planet. These microbes are drivers for many biogeochemical processes, and their enormous genetic potential is still not fully explored or…
RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like…
Reconstructing a dynamic scene from image inputs is a fundamental computer vision task with many downstream applications. Despite recent advancements, existing approaches still struggle to achieve high-quality reconstructions from unseen…
This work introduces the Re$^{\text{2}}$MaP method, which generates expert-quality macro placements through recursively prototyping and packing tree-based relocating. We first perform multi-level macro grouping and PPA-aware cell clustering…
We present MapReader, a free, open-source software library written in Python for analyzing large map collections (scanned or born-digital). This library transforms the way historians can use maps by turning extensive, homogeneous map sets…