ArticlePeerJ2016
Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads.
Article in PeerJ, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Whole genome sequencing, assembly and annotation of the Southern Ground Hornbill - Bucorvus leadbeateri.Scientific data · 2025Article
- Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT andGenome research · 2024Article
- Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors.PeerJ · 2024Article
- DeepCorr: a novel error correction method for 3GS long reads based on deep learning.PeerJ. Computer science · 2024Article
- Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii.Nature communications · 2022Article
- QuasiSeq: profiling viral quasispecies via self-tuning spectral clustering with PacBio long sequencing reads.Bioinformatics (Oxford, England) · 2022Article
- Article
- High-Quality Genome Assembly ofFrontiers in plant science · 2022Article
- Evolutionary transition to XY sex chromosomes associated with Y-linked duplication of a male hormone gene in a terrestrial isopod.Heredity · 2021Article
- The genome of Nautilus pompilius illuminates eye evolution and biomineralization.Nature ecology & evolution · 2021Article
- Draft Genome of the Mirrorwing Flyingfish (Frontiers in genetics · 2021Article
- Sequencing DNA with nanopores: Troubles and biases.PloS one · 2021Article
- [Reconstruction of tumor clonal haplotypes based on an improved spanning algorithm].Nan fang yi ke da xue xue bao = Journal of Southern Medical University · 2019Article
- New High-Quality Draft Genome of the Brown Rot Fungal Pathogen Monilinia fructicola.Genome biology and evolution · 2019Article
- Article
- Genome sequence of the brown rot fungal pathogen Monilinia fructigena.BMC research notes · 2018Article
- The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.Nature genetics · 2018Article
- Fast and accurate de novo genome assembly from long uncorrected reads.Genome research · 2017Article
- Genome Sequences ofGenome announcements · 2017Article
- DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation. The third generation sequencing (3GS) technology generates long sequences of thousands of bases. However, its current error rates are estimated in the range of 15-40%, significantly higher than those of the prevalent next generation sequencing (NGS) technologies (less than 1%). Fundamental bioinformatics tasks such as de novo genome assembly and variant calling require high-quality sequences that need to be extracted from these long but erroneous 3GS sequences. Results. We describe a versatile and efficient linear complexity consensus algorithm Sparc to facilitate de novo genome assembly. Sparc builds a sparse k-mer graph using a collection of sequences from a targeted genomic region. The heaviest path which approximates the most likely genome sequence is searched through a sparsity-induced reweighted graph as the consensus sequence. Sparc supports using NGS and 3GS data together, which leads to significant improvements in both cost efficiency and computational efficiency. Experiments with Sparc show that our algorithm can efficiently provide high-quality consensus sequences using both PacBio and Oxford Nanopore sequencing technologies. With only 30× PacBio data, Sparc can reach a consensus with error rate <0.5%. With the more challenging Oxford Nanopore data, Sparc can also achieve similar error rate when combined with NGS data. Compared with the existing approaches, Sparc calculates the consensus with higher accuracy, and uses approximately 80% less memory and time. Availability. The source code is available for download at https://github.com/yechengxi/Sparc.
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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.