ArticleBioinformatics (Oxford, England)2015
De novo meta-assembly of ultra-deep sequencing data.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed.
- Diversity of lncRNAs in the pan-transcriptome of maize inbred lines.BMC genomics · 2026Article
- The digestion and dietary carbohydrate pathway contains 100% gene mutations enrichment among 117 patients with major depressive disorder.Frontiers in psychiatry · 2024Article
- Complete mitochondrial genome and draft chloroplastic genome ofMitochondrial DNA. Part B, Resources · 2023Article
- Complete Genome Sequences of Four Pseudomonas aeruginosa Bacteriophages: Kara-mokiny 8, Kara-mokiny 13, Kara-mokiny 16, and Boorn-mokiny 1.Microbiology resource announcements · 2022Article
- The Genome Sequence of the OctocoralG3 (Bethesda, Md.) · 2020Article
- ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.BMC bioinformatics · 2020Article
- The orphan nuclear receptor estrogen-related receptor beta (ERRβ) in triple-negative breast cancer.Breast cancer research and treatment · 2020Article
- Review
- Article
- Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies.PloS one · 2019Article
- Sequana coverage: detection and characterization of genomic variations using running median and mixture models.GigaScience · 2018Article
- Comparative analysis of de novo assemblers for variation discovery in personal genomes.Briefings in bioinformatics · 2018Article
- Spherical: an iterative workflow for assembling metagenomic datasets.BMC bioinformatics · 2018Article
- Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations.Marine drugs · 2017Review
- Whole genome sequencing ofPeerJ · 2017Article
- Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist's Perspective - Not Only Size Matters!PloS one · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledWe introduce a new divide and conquer approach to deal with the problem of de novo genome assembly in the presence of ultra-deep sequencing data (i.e. coverage of 1000x or higher). Our proposed meta-assembler Slicembler partitions the input data into optimal-sized 'slices' and uses a standard assembly tool (e.g. Velvet, SPAdes, IDBA_UD and Ray) to assemble each slice individually. Slicembler uses majority voting among the individual assemblies to identify long contigs that can be merged to the consensus assembly. To improve its efficiency, Slicembler uses a generalized suffix tree to identify these frequent contigs (or fraction thereof). Extensive experimental results on real ultra-deep sequencing data (8000x coverage) and simulated data show that Slicembler significantly improves the quality of the assembly compared with the performance of the base assembler. In fact, most of the times, Slicembler generates error-free assemblies. We also show that Slicembler is much more resistant against high sequencing error rate than the base assembler. AVAILABILITY AND IMPLEMENTATION: Slicembler can be accessed at http://slicembler.cs.ucr.edu/.
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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.