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Shannon: An Information-Optimal de Novo RNA-Seq Assembler

https://doi.org/10.1101/039230
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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A Mathematical Theory of Communication
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inferredcites →https://doi.org/10.1007/bf01188580openalex-snapshot
Combinatorial algorithms for DNA sequence assembly
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Genomic mapping by fingerprinting random clones: A mathematical analysis
inferredcites →https://doi.org/10.1038/nbt.1621openalex-snapshot
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
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inferredcites →https://doi.org/10.1038/nbt.3122openalex-snapshot
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
inferredcites →https://doi.org/10.1038/nmeth.1517openalex-snapshot
De novo assembly and analysis of RNA-seq data
inferredcites →https://doi.org/10.1038/nmeth.2251openalex-snapshot
Streaming fragment assignment for real-time analysis of sequencing experiments
inferredcites →https://doi.org/10.1056/nejmoa1301689openalex-snapshot
Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
inferredcites →https://doi.org/10.1073/pnas.1320101110openalex-snapshot
Characterization of the human ESC transcriptome by hybrid sequencing
inferredcites →https://doi.org/10.1073/pnas.1400447111openalex-snapshot
Defining a personal, allele-specific, and single-molecule long-read transcriptome
inferredcites →https://doi.org/10.1089/cmb.2009.0047openalex-snapshot
Maximum Likelihood Genome Assembly
inferredcites →https://doi.org/10.1089/cmb.2011.0171openalex-snapshot
IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btr011openalex-snapshot
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inferredcites →https://doi.org/10.1093/bioinformatics/bts094openalex-snapshot
Oases:robustde novoRNA-seq assembly across the dynamic range of expression levels
inferredcites →https://doi.org/10.1093/bioinformatics/btu077openalex-snapshot
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
inferredcites →https://doi.org/10.1093/bioinformatics/btu317openalex-snapshot
Efficient RNA isoform identification and quantification from RNA-Seq data with network flows
inferredcites →https://doi.org/10.1093/nar/gkt215openalex-snapshot
Probabilistic error correction for RNA sequencing
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1186/1471-2105-14-s5-s15openalex-snapshot
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Optimal assembly for high throughput shotgun sequencing
inferredcites →https://doi.org/10.1186/gb-2010-11-11-r116openalex-snapshot
Quake: quality-aware detection and correction of sequencing errors
inferredcites →https://doi.org/10.1186/gb-2010-11-4-116openalex-snapshot
Phenotypic connections in surprising places
inferredcites →https://doi.org/10.1371/journal.pone.0130821openalex-snapshot
QuorUM: An Error Corrector for Illumina Reads

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inferred← citeshttps://doi.org/10.1101/2020.09.28.317594openalex-snapshot
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inferred← citeshttps://doi.org/10.1101/2022.01.02.473666openalex-snapshot
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inferred← citeshttps://doi.org/10.1109/tit.2018.2809001openalex-snapshot
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inferred← citeshttps://doi.org/10.1109/tmbmc.2023.3336254openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/1755-0998.13156openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/mec.17552openalex-snapshot
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inferred← citeshttps://doi.org/10.1145/3571723openalex-snapshot
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inferred← citeshttps://doi.org/10.1152/ajprenal.00067.2017openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12859-024-05663-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12862-019-1410-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12862-021-01944-0openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12864-018-5034-xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s13059-022-02624-yopenalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0232946openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0239381openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/genes12070953openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/genes12091423openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/ht8040020openalex-snapshot
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Peer Review #1 of "The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.5428v0.1/reviews/2openalex-snapshot
Peer Review #2 of "The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.5428v0.1/reviews/3openalex-snapshot
Peer Review #3 of "The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.5428v0.2/reviews/1openalex-snapshot
Peer Review #1 of "The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.5428v0.2/reviews/2openalex-snapshot
Peer Review #2 of "The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.5428openalex-snapshot
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly
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