ArticleEvolutionary bioinformatics online2018
A Comprehensive Study of De Novo Genome Assemblers: Current Challenges and Future Prospective.
Article in Evolutionary bioinformatics online, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Article
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- Environmental community transcriptomics: strategies and struggles.Briefings in functional genomics · 2025Review
- A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes.Nucleic acids research · 2024Article
- MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge.Genome biology · 2024Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge.bioRxiv : the preprint server for biology · 2024Article
- Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella.Scientific reports · 2023Article
- Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses.Viruses · 2023Review
- From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research.Life (Basel, Switzerland) · 2022Review
- Migrating to Long-Read Sequencing for Clinical RoutineCancer informatics · 2022Article
- Ten simple rules for getting started with command-line bioinformatics.PLoS computational biology · 2021Article
- Article
- Wood transcriptome analysis and expression variation of lignin biosynthetic pathway transcripts inJournal of biosciences · 2021Article
- Article
- Article
- A Customizable Analysis Flow in Integrative Multi-Omics.Biomolecules · 2020Review
- The effect of variant interference on de novo assembly for viral deep sequencing.BMC genomics · 2020Article
- instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder.Genome biology · 2020Article
- A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes.NAR genomics and bioinformatics · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCurrent advancements in next-generation sequencing technology have made possible to sequence whole genome but assembling a large number of short sequence reads is still a big challenge. In this article, we present the comparative study of seven assemblers, namely, ABySS, Velvet, Edena, SGA, Ray, SSAKE, and Perga, using prokaryotic and eukaryotic paired-end as well as single-end data sets from Illumina platform.
resultsResults showed that in case of single-end data sets, Velvet and ABySS outperformed in all the seven assemblers with comparatively low assembling time and high genome fraction. Velvet consumed the least amount of memory than any other assembler. In case of paired-end data sets, Velvet consumed least amount of time and produced high genome fraction after ABySS and Ray. In terms of low memory usage, SGA and Edena outperformed in all the assemblers. Ray also showed good genome fraction; however, extremely high assembling time consumed by the Ray might make it prohibitively slow on larger data sets of single and paired-end data.
conclusionsOur comparison study will provide assistance to the scientists for selecting the suitable assembler according to their data sets and will also assist the developers to upgrade or develop a new assembler for de novo assembling.
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