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Towards selective-alignment: Bridging the accuracy gap between alignment-based and alignment-free transcript quantification

https://doi.org/10.1101/138800
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What this work says

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

inferredcites →https://doi.org/10.1038/nature12531openalex-snapshot
Transcriptome and genome sequencing uncovers functional variation in humans
inferredcites →https://doi.org/10.1038/nbt.2862openalex-snapshot
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
inferredcites →https://doi.org/10.1038/nbt.2957openalex-snapshot
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
inferredcites →https://doi.org/10.1038/nbt.3519openalex-snapshot
Near-optimal probabilistic RNA-seq quantification
inferredcites →https://doi.org/10.1038/nmeth.3317openalex-snapshot
HISAT: a fast spliced aligner with low memory requirements
inferredcites →https://doi.org/10.1038/nmeth.4197openalex-snapshot
Salmon provides fast and bias-aware quantification of transcript expression
inferredcites →https://doi.org/10.1073/pnas.1419161111openalex-snapshot
rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btq057openalex-snapshot
Fast and SNP-tolerant detection of complex variants and splicing in short reads
inferredcites →https://doi.org/10.1093/bioinformatics/bts505openalex-snapshot
RazerS 3: Faster, fully sensitive read mapping
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btw277openalex-snapshot
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes
inferredcites →https://doi.org/10.1093/bioinformatics/btw371openalex-snapshot
deBGA: read alignment with de Bruijn graph-based seed and extension
inferredcites →https://doi.org/10.1093/bioinformatics/btw753openalex-snapshot
Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance
inferredcites →https://doi.org/10.1093/bioinformatics/btx106openalex-snapshot
Pseudoalignment for metagenomic read assignment
inferredcites →https://doi.org/10.1093/bioinformatics/btx262openalex-snapshot
Improved data-driven likelihood factorizations for transcript abundance estimation
inferredcites →https://doi.org/10.1093/nar/gkt005openalex-snapshot
Fast and accurate read mapping with approximate seeds and multiple backtracking
inferredcites →https://doi.org/10.1093/nar/gkt214openalex-snapshot
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
inferredcites →https://doi.org/10.1093/nar/gkv1157openalex-snapshot
Ensembl 2016
inferredcites →https://doi.org/10.1101/007427openalex-snapshot
Butter: High-precision genomic alignment of small RNA-seq data
inferredcites →https://doi.org/10.1101/011650openalex-snapshot
FusionCatcher – a tool for finding somatic fusion genes in paired-end RNA-sequencing data
inferredcites →https://doi.org/10.1101/gr.078212.108openalex-snapshot
Mapping short DNA sequencing reads and calling variants using mapping quality scores
inferredcites →https://doi.org/10.1137/0222058openalex-snapshot
Suffix Arrays: A New Method for On-Line String Searches
inferredcites →https://doi.org/10.1145/316542.316550openalex-snapshot
A fast bit-vector algorithm for approximate string matching based on dynamic programming
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1186/s13073-015-0167-xopenalex-snapshot
JAFFA: High sensitivity transcriptome-focused fusion gene detection
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
inferredcites →https://doi.org/10.7554/elife.11752openalex-snapshot
A new view of transcriptome complexity and regulation through the lens of local splicing variations

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s00125-023-05896-6openalex-snapshot
Methylation of histone H3 lysine 4 is required for maintenance of beta cell function in adult mice
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty292openalex-snapshot
A space and time-efficient index for the compacted colored de Bruijn graph
inferred← citeshttps://doi.org/10.1186/s13059-020-02151-8openalex-snapshot
Alignment and mapping methodology influence transcript abundance estimation
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