التفاصيل البيبلوغرافية
| العنوان: |
Streamlining remote nanopore data access with slow5curl |
| المؤلفون: |
Wong, Bonson, Ferguson, James M, Do, Jessica Y, Gamaarachchi, Hasindu, Deveson, Ira W |
| المساهمون: |
Australian Medical Research Futures Fund, Australian Research Council |
| المصدر: |
GigaScience ; volume 13 ; ISSN 2047-217X |
| بيانات النشر: |
Oxford University Press (OUP) |
| سنة النشر: |
2024 |
| مصطلحات موضوعية: |
Computer Science Applications, Health Informatics |
| الوصف: |
Background As adoption of nanopore sequencing technology continues to advance, the need to maintain large volumes of raw current signal data for reanalysis with updated algorithms is a growing challenge. Here we introduce slow5curl, a software package designed to streamline nanopore data sharing, accessibility, and reanalysis. Results Slow5curl allows a user to fetch a specified read or group of reads from a raw nanopore dataset stored on a remote server, such as a public data repository, without downloading the entire file. Slow5curl uses an index to quickly fetch specific reads from a large dataset in SLOW5/BLOW5 format and highly parallelized data access requests to maximize download speeds. Using all public nanopore data from the Human Pangenome Reference Consortium (>22 TB), we demonstrate how slow5curl can be used to quickly fetch and reanalyze raw signal reads corresponding to a set of target genes from each individual in large cohort dataset (n = 91), minimizing the time, egress costs, and local storage requirements for their reanalysis. Conclusions We provide slow5curl as a free, open-source package that will reduce frictions in data sharing for the nanopore community: https://github.com/BonsonW/slow5curlTest. |
| نوع الوثيقة: |
article in journal/newspaper |
| اللغة: |
English |
| DOI: |
10.1093/gigascience/giae016 |
| DOI: |
10.1093/gigascience/giae016/57223567/giae016.pdf |
| الإتاحة: |
https://doi.org/10.1093/gigascience/giae016Test |
| حقوق: |
https://creativecommons.org/licenses/by/4.0Test/ |
| رقم الانضمام: |
edsbas.B706EBC0 |
| قاعدة البيانات: |
BASE |
