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RNA-Bloom provides lightweight reference-free transcriptome assembly for single cells

https://doi.org/10.1101/701607
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What this work says

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

inferredcites →https://doi.org/10.1016/j.cell.2015.05.002openalex-snapshot
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
inferredcites →https://doi.org/10.1016/j.molcel.2017.06.003openalex-snapshot
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation
inferredcites →https://doi.org/10.1016/j.stem.2015.09.011openalex-snapshot
Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/nbt.3519openalex-snapshot
Near-optimal probabilistic RNA-seq quantification
inferredcites →https://doi.org/10.1038/ncomms14049openalex-snapshot
Massively parallel digital transcriptional profiling of single cells
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.2639openalex-snapshot
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
inferredcites →https://doi.org/10.1038/nmeth.4145openalex-snapshot
Effective detection of variation in single-cell transcriptomes using MATQ-seq
inferredcites →https://doi.org/10.1038/s41592-018-0082-3openalex-snapshot
BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq
inferredcites →https://doi.org/10.1093/bioinformatics/btw218openalex-snapshot
rnaQUAST: a quality assessment tool for de novo transcriptome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btw397openalex-snapshot
ntHash: recursive nucleotide hashing
inferredcites →https://doi.org/10.1093/bioinformatics/btw631openalex-snapshot
BASIC: BCR assembly from single cells
inferredcites →https://doi.org/10.1093/bioinformatics/btw832openalex-snapshot
ntCard: a streaming algorithm for cardinality estimation in genomics data
inferredcites →https://doi.org/10.1093/bioinformatics/bty203openalex-snapshot
B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle
inferredcites →https://doi.org/10.1093/gigascience/giz100openalex-snapshot
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
inferredcites →https://doi.org/10.1093/nar/gky182openalex-snapshot
Tn5Prime, a Tn5 based 5′ capture method for single cell RNA-seq
inferredcites →https://doi.org/10.1101/120295openalex-snapshot
STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq
inferredcites →https://doi.org/10.1101/gr.214346.116openalex-snapshot
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter
inferredcites →https://doi.org/10.1145/362686.362692openalex-snapshot
Space/time trade-offs in hash coding with allowable errors
inferredcites →https://doi.org/10.1155/2015/196591openalex-snapshot
Spaced Seed Data Structures forDe NovoAssembly
inferredcites →https://doi.org/10.1186/1471-2105-12-323openalex-snapshot
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
inferredcites →https://doi.org/10.1186/1748-7188-8-22openalex-snapshot
Space-efficient and exact de Bruijn graph representation based on a Bloom filter
inferredcites →https://doi.org/10.1186/s12920-018-0402-6openalex-snapshot
TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data
inferredcites →https://doi.org/10.1186/s13059-016-0881-8openalex-snapshot
A survey of best practices for RNA-seq data analysis
inferredcites →https://doi.org/10.1186/s13059-018-1496-zopenalex-snapshot
Single-cell RNAseq for the study of isoforms—how is that possible?
inferredcites →https://doi.org/10.1186/s13059-019-1676-5openalex-snapshot
Comparative analysis of sequencing technologies for single-cell transcriptomics
inferredcites →https://doi.org/10.1186/s13742-015-0089-yopenalex-snapshot
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.dib.2020.105166openalex-snapshot
Dataset for sequencing and de novo assembly of the European endangered white-clawed crayfish (Austropotamobius pallipes) abdominal muscle transcriptome
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz902openalex-snapshot
Fusion-Bloom: fusion detection in assembled transcriptomes
inferred← citeshttps://doi.org/10.1093/gigascience/giz100openalex-snapshot
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
inferred← citeshttps://doi.org/10.1101/710699openalex-snapshot
Terminitor: Cleavage Site Prediction Using Deep Learning Models
inferred← citeshttps://doi.org/10.1104/pp.20.00522openalex-snapshot
Complete Biosynthesis of the Anti-Diabetic Plant Metabolite Montbretin A
inferred← citeshttps://doi.org/10.1104/pp.20.00593openalex-snapshot
Terpene Synthases and Terpene Variation in Cannabis sativa
inferred← citeshttps://doi.org/10.1134/s1068162024030129openalex-snapshot
Bioinformatic Approaches for the Detection of Fusion Genes and trans-Splicing Products (A Review)
inferred← citeshttps://doi.org/10.1186/s12859-020-03614-2openalex-snapshot
Extending rnaSPAdes functionality for hybrid transcriptome assembly
inferred← citeshttps://doi.org/10.31857/s0132342324030033openalex-snapshot
Bioinformatic approaches for detection of fusion genes and trans-splicing products
inferred← citeshttps://doi.org/10.3389/fgene.2021.665888openalex-snapshot
A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells
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