相似文献
1
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data.
Bioinformatics. 2012 Jul 15;28(14):1923-4. doi: 10.1093/bioinformatics/bts272. Epub 2012 May 4.
2
OSA: a fast and accurate alignment tool for RNA-Seq.
Bioinformatics. 2012 Jul 15;28(14):1933-4. doi: 10.1093/bioinformatics/bts294. Epub 2012 May 15.
3
SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis.
BMC Bioinformatics. 2016 Feb 4;17:66. doi: 10.1186/s12859-016-0923-y.
4
Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data.
BMC Genomics. 2012 Aug 14;13:392. doi: 10.1186/1471-2164-13-392.
5
rnaQUAST: a quality assessment tool for de novo transcriptome assemblies.
Bioinformatics. 2016 Jul 15;32(14):2210-2. doi: 10.1093/bioinformatics/btw218. Epub 2016 Apr 23.
6
De Novo Plant Transcriptome Assembly and Annotation Using Illumina RNA-Seq Reads.
Methods Mol Biol. 2019;1933:265-275. doi: 10.1007/978-1-4939-9045-0_16.
7
Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms.
BMC Bioinformatics. 2016 Dec 9;17(1):525. doi: 10.1186/s12859-016-1406-x.
8
Updates to the RMAP short-read mapping software.
Bioinformatics. 2009 Nov 1;25(21):2841-2. doi: 10.1093/bioinformatics/btp533. Epub 2009 Sep 7.
9
Transcript Profiling Using Long-Read Sequencing Technologies.
Methods Mol Biol. 2018;1783:121-147. doi: 10.1007/978-1-4939-7834-2_6.
10
READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data.
Bioinformatics. 2014 Dec 1;30(23):3421-3. doi: 10.1093/bioinformatics/btu533. Epub 2014 Aug 13.
引用本文的文献
1
Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.
Methods Mol Biol. 2025;2883:231-255. doi: 10.1007/978-1-0716-4290-0_10.
2
Novornabreak: Local Assembly for Novel Splice Junction and Fusion Transcript Detection from RNA-Seq Data.
J Bioinform Syst Biol. 2023;6(2):74-81. doi: 10.26502/jbsb.5107050. Epub 2023 Apr 4.
3
Single-cell gene fusion detection by scFusion.
Nat Commun. 2022 Feb 28;13(1):1084. doi: 10.1038/s41467-022-28661-6.
4
ChiTaH: a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data.
NAR Genom Bioinform. 2021 Nov 26;3(4):lqab112. doi: 10.1093/nargab/lqab112. eCollection 2021 Dec.
5
LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.
BMC Genomics. 2020 Dec 29;21(Suppl 11):793. doi: 10.1186/s12864-020-07207-4.
6
FusionScan: accurate prediction of fusion genes from RNA-Seq data.
Genomics Inform. 2019 Sep;17(3):e26. doi: 10.5808/GI.2019.17.3.e26. Epub 2019 Jul 23.
7
Alignment-free filtering for cfNA fusion fragments.
Bioinformatics. 2019 Jul 15;35(14):i225-i232. doi: 10.1093/bioinformatics/btz346.
8
A fast detection of fusion genes from paired-end RNA-seq data.
BMC Genomics. 2018 Nov 1;19(1):786. doi: 10.1186/s12864-018-5156-1.
9
SeqOthello: querying RNA-seq experiments at scale.
Genome Biol. 2018 Oct 19;19(1):167. doi: 10.1186/s13059-018-1535-9.
10
Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome.
Nat Commun. 2018 Sep 27;9(1):3962. doi: 10.1038/s41467-018-06485-7.
本文引用的文献
1
Next-generation transcriptome assembly.
Nat Rev Genet. 2011 Sep 7;12(10):671-82. doi: 10.1038/nrg3068.
2
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
Genome Biol. 2011 Aug 11;12(8):R72. doi: 10.1186/gb-2011-12-8-r72.
3
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.
PLoS Comput Biol. 2011 May;7(5):e1001138. doi: 10.1371/journal.pcbi.1001138. Epub 2011 May 19.
4
Computational methods for transcriptome annotation and quantification using RNA-seq.
Nat Methods. 2011 Jun;8(6):469-77. doi: 10.1038/nmeth.1613. Epub 2011 May 27.
5
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.
6
Mapping copy number variation by population-scale genome sequencing.
Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.
7
Identification of fusion genes in breast cancer by paired-end RNA-sequencing.
Genome Biol. 2011;12(1):R6. doi: 10.1186/gb-2011-12-1-r6. Epub 2011 Jan 19.
8
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.
Genome Biol. 2010;11(10):R104. doi: 10.1186/gb-2010-11-10-r104. Epub 2010 Oct 21.
9
De novo assembly and analysis of RNA-seq data.
Nat Methods. 2010 Nov;7(11):909-12. doi: 10.1038/nmeth.1517. Epub 2010 Oct 10.
10
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2.
Zotero 插件