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https://hdl.handle.net/10356/181004
Title: | LSTrAP-denovo: automated generation of transcriptome atlases for eukaryotic species without genomes | Authors: | Lim, Peng Ken Wang, Ruoxi Mutwil, Marek |
Keywords: | Medicine, Health and Life Sciences | Issue Date: | 2024 | Source: | Lim, P. K., Wang, R. & Mutwil, M. (2024). LSTrAP-denovo: automated generation of transcriptome atlases for eukaryotic species without genomes. Physiologia Plantarum, 176(4), e14407-. https://dx.doi.org/10.1111/ppl.14407 | Project: | MOE-MOET32022-0002 | Journal: | Physiologia Plantarum | Abstract: | Despite the abundance of species with transcriptomic data, a significant number of species still lack sequenced genomes, making it difficult to study gene function and expression in these organisms. While de novo transcriptome assembly can be used to assemble protein-coding transcripts from RNA-sequencing (RNA-seq) data, the datasets used often only feature samples of arbitrarily selected or similar experimental conditions, which might fail to capture condition-specific transcripts. We developed the Large-Scale Transcriptome Assembly Pipeline for de novo assembled transcripts (LSTrAP-denovo) to automatically generate transcriptome atlases of eukaryotic species. Specifically, given an NCBI TaxID, LSTrAP-denovo can (1) filter undesirable RNA-seq accessions based on read data, (2) select RNA-seq accessions via unsupervised machine learning to construct a sample-balanced dataset for download, (3) assemble transcripts via over-assembly, (4) functionally annotate coding sequences (CDS) from assembled transcripts and (5) generate transcriptome atlases in the form of expression matrices for downstream transcriptomic analyses. LSTrAP-denovo is easy to implement, written in Python, and is freely available at https://github.com/pengkenlim/LSTrAP-denovo/. | URI: | https://hdl.handle.net/10356/181004 | ISSN: | 0031-9317 | DOI: | 10.1111/ppl.14407 | Schools: | School of Biological Sciences | Rights: | © 2024 Scandinavian Plant Physiology Society. All rights reserved. | Fulltext Permission: | none | Fulltext Availability: | No Fulltext |
Appears in Collections: | SBS Journal Articles |
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