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- Title
KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition.
- Authors
Labani, Mahdieh; Beheshti, Amin; Lovell, Nigel H.; Alinejad-Rokny, Hamid; Afrasiabi, Ali
- Abstract
Here we developed KARAJ, a fast and flexible Linux command-line tool to automate the end-to-end process of querying and downloading a wide range of genomic and transcriptomic sequence data types. The input to KARAJ is a list of PMCIDs or publication URLs or various types of accession numbers to automate four tasks as follows; firstly, it provides a summary list of accessible datasets generated by or used in these scientific articles, enabling users to select appropriate datasets; secondly, KARAJ calculates the size of files that users want to download and confirms the availability of adequate space on the local disk; thirdly, it generates a metadata table containing sample information and the experimental design of the corresponding study; and lastly, it enables users to download supplementary data tables attached to publications. Further, KARAJ provides a parallel downloading framework powered by Aspera connect which reduces the downloading time significantly.
- Subjects
ACQUISITION of data; MULTIPROCESSORS; TRANSCRIPTOMES; DOWNLOADING; METADATA; INFORMATION design; EXPERIMENTAL design
- Publication
International Journal of Molecular Sciences, 2022, Vol 23, Issue 22, p14418
- ISSN
1661-6596
- Publication type
Article
- DOI
10.3390/ijms232214418