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 …

We introduce Scallop, an accurate reference-based transcript assembler that improves
reconstruction of multi-exon and lowly expressed transcripts. Scallop preserves long-range …

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 …

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 …

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 …

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 …

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 …

Background The performance of RNA sequencing (RNA-seq) aligners and assemblers
varies greatly across different organisms and experiments, and often the optimal approach is …

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 …

Massively parallel sequencing of cDNA has enabled deep and efficient probing of
transcriptomes. Current approaches for transcript reconstruction from such data often rely on …