StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Methods used to sequence the transcriptome often produce more than 200 million short
sequences. We introduce StringTie, a computational method that applies a network flow …
sequences. We introduce StringTie, a computational method that applies a network flow …
Accurate assembly of transcripts through phase-preserving graph decomposition
M Shao, C Kingsford - Nature biotechnology, 2017 - nature.com
We introduce Scallop, an accurate reference-based transcript assembler that improves
reconstruction of multi-exon and lowly expressed transcripts. Scallop preserves long-range …
reconstruction of multi-exon and lowly expressed transcripts. Scallop preserves long-range …
[HTML][HTML] TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs
Transcriptome assemblers aim to reconstruct full-length transcripts from RNA-seq data. We
present TransComb, a genome-guided assembler developed based on a junction graph …
present TransComb, a genome-guided assembler developed based on a junction graph …
[HTML][HTML] Improved transcriptome assembly using a hybrid of long and short reads with StringTie
Short-read RNA sequencing and long-read RNA sequencing each have their strengths and
weaknesses for transcriptome assembly. While short reads are highly accurate, they are …
weaknesses for transcriptome assembly. While short reads are highly accurate, they are …
[HTML][HTML] Transcriptome assembly from long-read RNA-seq alignments with StringTie2
RNA sequencing using the latest single-molecule sequencing instruments produces reads
that are thousands of nucleotides long. The ability to assemble these long reads can greatly …
that are thousands of nucleotides long. The ability to assemble these long reads can greatly …
[HTML][HTML] Bridger: a new framework for de novo transcriptome assembly using RNA-seq data
We present a new de novo transcriptome assembler, Bridger, which takes advantage of
techniques employed in Cufflinks to overcome limitations of the existing de novo …
techniques employed in Cufflinks to overcome limitations of the existing de novo …
[HTML][HTML] CLASS: constrained transcript assembly of RNA-seq reads
Background RNA-seq has revolutionized our ability to survey the cellular transcriptome in
great detail. However, while several approaches have been developed, the problem of …
great detail. However, while several approaches have been developed, the problem of …
[PDF][PDF] Leveraging multiple transcriptome assembly methods for improved gene structure annotation
Background The performance of RNA sequencing (RNA-seq) aligners and assemblers
varies greatly across different organisms and experiments, and often the optimal approach is …
varies greatly across different organisms and experiments, and often the optimal approach is …
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
Y Xie, G Wu, J Tang, R Luo, J Patterson, S Liu… - …, 2014 - academic.oup.com
Motivation: Transcriptome sequencing has long been the favored method for quickly and
inexpensively obtaining a large number of gene sequences from an organism with no …
inexpensively obtaining a large number of gene sequences from an organism with no …
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Massively parallel sequencing of cDNA has enabled deep and efficient probing of
transcriptomes. Current approaches for transcript reconstruction from such data often rely on …
transcriptomes. Current approaches for transcript reconstruction from such data often rely on …