Biology subjects

Chhugani, K.

Publications and source records attributed to Chhugani, K..

4 recordsLinked to original sources

bioRxiv2025

Robust software development practices improve citations of RNA-seq tools

RNA sequencing (RNA-seq) has emerged as an exemplary technology in biology and clinical applications, offering a crucial complement to other transcriptomic profiling protocols due to its high sensitivity, precision, and accuracy in characterizing transcriptomes. However, the rapid proliferation of RNA-seq tools necessitates the adoption of robust software development practices. Such development underscores the critical need to examine how RNA-seq tools are developed, maintained, and distributed; and whether the data they generate is reproducible as all of these factors are essential for ensuring software reliability, transparency, and trust in scientific findings. We conducted a comprehensive assessment of 434 RNA-seq tools developed between 2008 and 2024, categorizing them based on the type of analysis they perform. Our evaluation encompassed their software development and distribution methodologies, as well as the attributes contributing to their widespread adoption and dependability within the biomedical community, which were quantified by factors such as package manager availability, containerization, multithreading support, documentation quality, and inclusion of example datasets. Our findings establish the first documented positive association between rigorous software development practices and their adoption of published RNA-seq tools as measured by citations (Mann-Whitney U test, p-value = 4.9 x 10-26). By identifying key characteristics of widely adopted software, our findings guide developing robust and user-friendly RNA-seq tools, thereby reinforcing the call for rigorous community-wide standards.

bioinformatics↗

bioRxiv2025

Assessing genomic reproducibility of read alignment tools

Genomic research relies on accurate and reproducible computational analyses of DNA sequencing data to draw reliable biological conclusions. Read mapping, the process of aligning reads to a reference genome, is central to many applications, including variant detection and comparative genomics. While several tools have been developed for this task, genomic reproducibility1, defined as the consistency of results across replicates, remains underexplored. Here, we address this question by introducing a methodology based on synthetic replicates of sequencing data, generated by perturbing the original reads through shuffling, reverse complementing, or combined shuffling and reverse complementing. Our approach is able to simulate variability observed across sequencing runs due to differences in library preparation techniques. We evaluated the reproducibility of eight alignment tools (BWA-MEM22, Bowtie23, HISAT24, minimap25, NextGenMap6, SNAP7, SMALT7,8 and Subread9) under these perturbations using whole-genome sequencing (WGS) data. Synthetic replicates were aligned and compared to the original sample to quantify discrepancies. Mapping accuracy changes ranged from 0.0001% to 4.4% for primary reads, which are alignments not marked as secondary, supplementary, or duplicates, and up to 12.2% for high-quality primary reads. For primary reads, the percentage of reads commonly mapped in both the original and synthetic replicate ranged from 91.66% to 100% relative to the total number of mapped reads in the original dataset. High-quality filtering improved consistency, though some tools still failed to recover more than 70% of the original alignments. Within the set of common reads, the incidence of inconsistent mappings was as high as 13.53% for primary reads and 6.73% for high-quality primary reads. Bowtie 2 was fully reproducible under the shuffling replicate, Subread was fully reproducible under the reverse-complement replicate, whereas NextGenMap exhibited only minor inconsistencies. By contrast, SNAP and minimap2 displayed the most significant variability under reverse complementing. We further demonstrate that alignment inconsistencies propagate to the downstream task of calling structural genomic variants. Using Manta for structural-variant (SV) calling, we observed that Bowtie 2, HISAT2, and minimap2 maintained perfect SV concordance between original and replicate alignments, whereas other tools exhibited lower concordance, with Subread scoring only 87% concordance. In conclusion, our comprehensive evaluation demonstrates that synthetic perturbations reveal critical differences in how alignment tools handle technical variability and how these differences propagate to downstream variant analyses, underscoring the necessity of incorporating reproducibility benchmarks into the selection and validation of read mappers to ensure robust and reliable genomic interpretations.

bioinformatics↗

bioRxiv2022

Unlocking the microblogging potential for science and medicine

Microblogging platform Twitter allows researchers to showcase their work, receive constructive feedback, find jobs, and build scientific collaborations. While existing literature has analyzed the benefits of Twitter in the development and distribution of scientific knowledge, most of the studies only took into account a limited number of researchers, which affected the generalizability of derived results. Our study analyzed the activity of 6,000 biomedical scientists on Twitter using data-driven approaches, a third of whom were female. Furthermore, we estimated that up to a quarter of the members of the scientific community are engaged on Twitter. While the number of male scientists joining the microblogging platform every year has decreased, the number of female scientists has remained roughly the same. Scientists are very selective in who they are following as compared to the general public. We also found that the type of tweets and retweets one posts may affect the number of followers, specifically, that a moderate to high level of professionalism and a high level of positivity is correlated with followers count. Moreover, female scientists send fewer negative tweets as compared to male scientists (31.1% for females and 34.7% for males). Our analysis could provide insights and launch a conversation on the advantages and limitations of using Twitter for disseminating scientific information and engaging in constructive discussion and collaborations within the scientific community.

scientific communication and education↗

bioRxiv2021

Virtual meetings promise to eliminate the geographical and administrative barriers and increase accessibility, diversity, and inclusivity

The COVID-19 pandemic brought a new set of unprecedented challenges not only for healthcare, education, and everyday jobs but also in terms of academic conferences. In this study, we investigate the effect of the broad adoption of virtual platforms for academic conferences as a response to COVID-19 restrictions. We show that virtual platforms enable higher participation from underrepresented minority groups, increased inclusion, and broader geographic distribution. We also discuss emerging challenges associated with the virtual conference format resulting in a decreased engagement of social activities, limited possibilities of cross-fertilization between participants, and reduced peer-to-peer interactions. Lastly, we conclude that a novel comprehensive approach needs to be adopted by the conference organizers to ensure increased accessibility, diversity, and inclusivity of post-pandemic conferences. Our findings provide evidence favoring a hybrid format for future conferences, marrying the strength of both in-person and virtual platforms.

scientific communication and education↗