ArticleGenome biology2016
TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Minimum flow decomposition guided by saturating subflows.bioRxiv : the preprint server for biology · 2026Article
- Amaranth: enhanced single-cell transcript assembly via discriminative modelling of UMI reads and internal reads.Bioinformatics (Oxford, England) · 2026Article
- Data-driven AI system for learning how to run transcript assemblers.Genome biology · 2026Article
- Amaranth: Enhanced Single-Cell Transcript Assembly via Discriminative Modeling of UMI Reads and Internal Reads.bioRxiv : the preprint server for biology · 2025Article
- Boosting Transcript Assembly via Delineating Transcript Start and End Sites.bioRxiv : the preprint server for biology · 2025Article
- Accurate assembly of multiple RNA-seq samples with Aletsch.Bioinformatics (Oxford, England) · 2024Article
- StringFix: an annotation-guided transcriptome assembler improves the recovery of amino acid sequences from RNA-Seq reads.Genes & genomics · 2023Article
- Transcript assembly and annotations: Bias and adjustment.PLoS computational biology · 2023Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- OnACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2023Article
- Flnc: Machine Learning Improves the Identification of Novel Long Noncoding RNAs from Stand-Alone RNA-Seq Data.Non-coding RNA · 2022Article
- Bookend: precise transcript reconstruction with end-guided assembly.Genome biology · 2022Article
- Tiglon enables accurate transcriptome assembly via integrating mappings of different aligners.iScience · 2022Article
- Accurate assembly of multi-end RNA-seq data with Scallop2.Nature computational science · 2022Article
- Jumper enables discontinuous transcript assembly in coronaviruses.Nature communications · 2021Article
- CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.PLoS computational biology · 2021Article
- Exact transcript quantification over splice graphs.Algorithms for molecular biology : AMB · 2021Article
- TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers.Genome research · 2020Article
- More Accurate Transcript Assembly via Parameter Advising.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- Exploring Additional Valuable Information From Single-Cell RNA-Seq Data.Frontiers in cell and developmental biology · 2020Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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, weighted by a bin-packing strategy and paired-end information. A newly designed extension method based on weighted junction graphs can accurately extract paths representing expressed transcripts, whether they have low or high expression levels. Tested on both simulated and real datasets, TransComb demonstrates significant improvements in both recall and precision over leading assemblers, including StringTie, Cufflinks, Bayesembler, and Traph. In addition, it runs much faster and requires less memory on average. TransComb is available at http://sourceforge.net/projects/transcriptomeassembly/files/ .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.