SAGE: String-overlap Assembly of GEnomes

Ilie, Lucian; Haider, Bahlul; Molnar, Michael; Solis-Oba, Roberto

doi:10.1186/1471-2105-15-302

Cited by 9 publications

(8 citation statements)

References 29 publications

(47 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…A number of internal TSSs in the coding regions of genes was also detected, which further demonstrated a complex transcriptional architecture of C. difficile genome ( Supplementary Table S2, column I highlighted in blue, Figure 1B). In many cases, these internal TSS map to the genes with identified primary TSS in accordance with the mechanisms for internal transcription initiation by elongating RNAP complexes suggested in bacteria (Shao et al, 2014;Cuklina et al, 2016;Harden et al, 2016). Moreover, internal transcription initiation could be at the origin of 3 -end derived ncRNA as recently demonstrated in other bacterial species (Chao et al, 2012;Guo et al, 2014).…”

Section: Identification Of Two Promoters Upstream Genes and Internal supporting

confidence: 81%

Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile

et al. 2020

View full text Add to dashboard Cite

show abstract

Section: Identification Of Two Promoters Upstream Genes and Internal supporting

confidence: 81%

Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Table 1 gives the assembly statistics corresponding to this experiment. Comparable assembly results on this data were reported by Ilie et al (2014) , though in some cases we used more recent software releases (e.g. for SPAdes).…”

Section: Analysesmentioning

confidence: 78%

Misassembly detection using paired-end sequence reads and optical mapping data

et al. 2015

View full text Add to dashboard Cite

Motivation: A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes. We develop a method called misSEQuel that enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data. Our method also fulfills the critical need for open source computational methods for analyzing optical mapping data. We apply our method to various assemblies of the loblolly pine, Francisella tularensis, rice and budgerigar genomes. We generated and used stimulated optical mapping data for loblolly pine and F.tularensis and used real optical mapping data for rice and budgerigar.Results: Our results demonstrate that we detect more than 54% of extensively misassembled contigs and more than 60% of locally misassembled contigs in assemblies of F.tularensis and between 31% and 100% of extensively misassembled contigs and between 57% and 73% of locally misassembled contigs in assemblies of loblolly pine. Using the real optical mapping data, we correctly identified 75% of extensively misassembled contigs and 100% of locally misassembled contigs in rice, and 77% of extensively misassembled contigs and 80% of locally misassembled contigs in budgerigar.Availability and implementation: misSEQuel can be used as a post-processing step in combination with any genome assembler and is freely available at http://www.cs.colostate.edu/seq/.Contact: muggli@cs.colostate.eduSupplementary information: Supplementary data are available at Bioinformatics online.

show abstract

“…Genome assembly is a difficult problem that is far from being solved. A multitude of assemblers have been designed, see, e.g., [ 1 – 11 ].…”

Section: Introductionmentioning

confidence: 99%

LASER: Large genome ASsembly EvaluatoR

Khiste

Ilie

2015

BMC Res Notes

Self Cite

View full text Add to dashboard Cite

BackgroundGenome assembly is a fundamental problem with multiple applications. Current technological limitations do not allow assembling of entire genomes and many programs have been designed to produce longer and more reliable contigs. Assessing the quality of these assemblies and comparing those produced by different tools is essential in choosing the best ones. The QUAST program has become the current state-of-the-art in quality assessment of genome assemblies. The only drawback of QUAST is high time and memory usage for large genomes, e.g., over 4 days and 120 GB of RAM for a single human genome assembly.ResultsWe introduce LASER, a new tool for assembly evaluation that improves greatly the speed and memory requirements of QUAST. For a human genome assembly, LASER is 5.6 times faster than QUAST while using only half the memory; one human genome assembly is evaluated in 17 hours instead of 4 days. The code of LASER is based on that of QUAST and therefore inherits all its features.ConclusionsGenome assembly evaluation is an essential step in assessing the quality of an assembly that is too often done improperly, in part due to significant resource consumption. With the introduction of LASER, proper evaluation can be performed efficiently.

show abstract

SAGE: String-overlap Assembly of GEnomes

Cited by 9 publications

References 29 publications

Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile

Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile

Misassembly detection using paired-end sequence reads and optical mapping data

LASER: Large genome ASsembly EvaluatoR

Contact Info

Product

Resources

About