@article{minimap2,
author = {Li, Heng},
title = "{Minimap2: pairwise alignment for nucleotide sequences}",
journal = {Bioinformatics},
volume = {34},
number = {18},
pages = {3094-3100},
year = {2018},
month = {05},
abstract = "{Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15\\%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3–4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment.https://github.com/lh3/minimap2Supplementary data are available at Bioinformatics online.}",
issn = {1367-4803},
doi = {10.1093/bioinformatics/bty191},
url = {https://doi.org/10.1093/bioinformatics/bty191},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/34/18/3094/25731860/bty191\_suppl\_data.pdf},
}
@Manual{biocfilecache,
title = {BiocFileCache: Manage Files Across Sessions},
author = {Lori Shepherd and Martin Morgan},
year = {2021},
note = {R package version 2.0.0},
}
@Article{singlecellexperiment,
title = {Orchestrating single-cell analysis with Bioconductor},
author = {Robert Amezquita and Aaron Lun and Etienne Becht and Vince Carey and Lindsay Carpp and Ludwig Geistlinger and Federico Marini and Kevin Rue-Albrecht and Davide Risso and Charlotte Soneson and Levi Waldron and Herve Pages and Mike Smith and Wolfgang Huber and Martin Morgan and Raphael Gottardo and Stephanie Hicks},
year = {2020},
volume = {17},
pages = {137--145},
journal = {Nature Methods},
url = {https://www.nature.com/articles/s41592-019-0654-x},
}
@Manual{summarizedexperiment,
title = {SummarizedExperiment: SummarizedExperiment container},
author = {Martin Morgan and Valerie Obenchain and Jim Hester and Hervé Pagès},
year = {2020},
note = {R package version 1.20.0},
url = {https://bioconductor.org/packages/SummarizedExperiment},
}
@article {flames,
author = {Tian, Luyi and Jabbari, Jafar S. and Thijssen, Rachel and Gouil, Quentin and Amarasinghe, Shanika L. and Kariyawasam, Hasaru and Su, Shian and Dong, Xueyi and Law, Charity W. and Lucattini, Alexis and Chung, Jin D. and Naim, Timur and Chan, Audrey and Ly, Chi Hai and Lynch, Gordon S. and Ryall, James G. and Anttila, Casey J.A. and Peng, Hongke and Anderson, Mary Ann and Roberts, Andrew W. and Huang, David C.S. and Clark, Michael B. and Ritchie, Matthew E.},
title = {Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing},
elocation-id = {2020.08.10.243543},
year = {2020},
doi = {10.1101/2020.08.10.243543},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Alternative splicing shapes the phenotype of cells in development and disease. Long-read RNA-sequencing recovers full-length transcripts but has limited throughput at the single-cell level. Here we developed single-cell full-length transcript sequencing by sampling (FLT-seq), together with the computational pipeline FLAMES to overcome these issues and perform isoform discovery and quantification, splicing analysis and mutation detection in single cells. With FLT-seq and FLAMES, we performed the first comprehensive characterization of the full-length isoform landscape in single cells of different types and species and identified thousands of unannotated isoforms. We found conserved functional modules that were enriched for alternative transcript usage in different cell populations, including ribosome biogenesis and mRNA splicing. Analysis at the transcript-level allowed data integration with scATAC-seq on individual promoters, improved correlation with protein expression data and linked mutations known to confer drug resistance to transcriptome heterogeneity. Our methods reveal previously unseen isoform complexity and provide a better framework for multi-omics data integration.Competing Interest StatementThe authors have declared no competing interest.},
URL = {https://www.biorxiv.org/content/early/2020/08/10/2020.08.10.243543},
eprint = {https://www.biorxiv.org/content/early/2020/08/10/2020.08.10.243543.full.pdf},
journal = {bioRxiv}
}
@article{blaze,
title={Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE},
author={You, Yupei and Prawer, Yair DJ and Paoli-Iseppi, De and Hunt, Cameron PJ and Parish, Clare L and Shim, Heejung and Clark, Michael B and others},
journal={Genome Biology},
volume={24},
number={1},
pages={1--23},
year={2023},
publisher={BioMed Central}
}
@article{flexiplex,
title={Flexiplex: A versatile demultiplexer and search tool for omics data},
author={Davidson, Nadia M and Amin, Noorul and Min Hao, Ling and Wang, Changqing and Cheng, Oliver and Goeke, Jonathan M and Ritchie, Matthew E and Wu, Shuyi},
journal={bioRxiv},
pages={2023--08},
year={2023},
publisher={Cold Spring Harbor Laboratory}
}
@article{bambu,
title={Context-aware transcript quantification from long-read RNA-seq data with Bambu},
author={Chen, Ying and Sim, Andre and Wan, Yuk Kei and Yeo, Keith and Lee, Joseph Jing Xian and Ling, Min Hao and Love, Michael I and G{\"o}ke, Jonathan},
journal={Nature Methods},
pages={1--9},
year={2023},
publisher={Nature Publishing Group US New York}
}
