Related papers: LRez: C++ API and toolkit for analyzing and managi…
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.…
There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
A method for designing sequencing barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time sequencing is presented. The manuscript focuses on…
Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Accurate barcode detection and decoding in Identity documents is crucial for applications like security, healthcare, and education, where reliable data extraction and verification are essential. However, building robust detection models is…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
In modern software ecosystems, 1-day vulnerabilities pose significant security risks due to extensive code reuse. Identifying vulnerable functions in target binaries alone is insufficient; it is also crucial to determine whether these…
The complexity of code reviews has driven efforts to automate review comments, but prior approaches oversimplify this task by treating it as snippet-level code-to-text generation and relying on text similarity metrics like BLEU for…
Writing a readme is a crucial aspect of software development as it plays a vital role in managing and reusing program code. Though it is a pain point for many developers, automatically creating one remains a challenge even with the recent…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Modern distributed systems produce massive, heterogeneous logs essential for reliability, security, and anomaly detection. Converting these free-form messages into structured templates (log parsing) is challenging due to evolving formats…
Retrieval-augmented generation (RAG) combines knowledge from domain-specific sources into large language models to ground answer generation. Current RAG systems lack customizable visibility on the context documents and the model's…
Bam-readcount is a utility for generating low-level information about sequencing data at specific nucleotide positions. Originally designed to help filter genomic mutation calls, the metrics it outputs are useful as input for variant…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
We present BadgeX, a novel system integrating lightweight wearable IoT devices (smart badges/smartphones) with Large Language Models (LLMs) to enable real-time collaborative learning analytics. The system captures multimodal sensor data…
Large Language Models (LLMs) have demonstrated impressive capabilities in code generation. While an interactive feedback loop can improve performance, writing effective tests is a non-trivial task. Early multi-agent frameworks, such as…
Artificial intelligence (AI) provides an alternative way to design channel coding with affordable complexity. However, most existing studies can only learn codes for a given size and rate, typically defined by a fixed network architecture…
Data structures and algorithms are essential building blocks for programs, and \emph{distributed data structures}, which automatically partition data across multiple memory locales, are essential to writing high-level parallel programs.…