/17/$ © IEEE Our proposed pipeline is implemented on BGI Online to provide a user-friendly graphical interface Index Terms—pipeline, single cell sequencing, copy number variation detection, BGI Online. ISBN: pp: Yuwen Zhou, BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China. Aodan Xu. (4)BGI Genomics, BGI-Shenzhen, Shenzhen, , China. association study on pulmonary TB patients and healthy controls.

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Every module in the pipeline is designed to achieve unitary task, and is unattached, thus facilitating user-customized applications. Paired-end information was used to cluster semi-unmapped reads into the gap regions, and then these reads were locally assembled into a consensus.

Trinity version r was run with minimum-assembled-contig-length-to-report set to 55090 The pipeline is open for public usage and its address is http: For the most complex paths, only the top scoring transcripts are retained.

Genome-wide association study identifies two risk loci for tuberculosis in Han Chinese.

Alternative splicing establishes multiple successive linkages from a unique contig. This might result in a more complete transcript set, but it may also introduce redundancy; ii iterate different k -mer DBG assemblies during contig construction. Assemblers such as Cufflinks Trapnell et al. SOAPdenovo-Trans incorporates the error-removal model from Trinity and the robust heuristic graph traversal method from Oases.

In addition, we use a strict transitive reduction method to simplify the scaffolding graphs, and provide more accurate results. If so, it would necessarily alter the types of issues faced by transcriptome analysis.

Published by Oxford University Press. Notice that the assembly-to-annotation 50990 are plotted in reverse, from large to small. We first assessed the 590 demands of the three software programs with regard to peak memory and time Table 1. We used the terms series-A and series-B to denote the sets of transcripts that included or excluded putative alternative splice forms, respectively.


In these situations, de novo assembly is required. To assess the 5009 of these changes, we evaluated all three assemblers on bvi and mouse, which have established transcriptome data linked to genome annotations produced over the last decade. It also does not allow for alternative splicing.

In contrast to Figure 2where we showed a distribution, here we plot a cumulant. Adopting and improving on concepts from Trinity and Oases resolved these issues.

A copy-number variation detection pipeline for single cell sequencing data on BGI online

We noticed that the assemblers often produced multiple artifactual transcripts as a result of minor substitution 50090 in the raw input data.

Each sub-graph consists of a set of transcripts alternative splice forms that share common exons. BioinformaticsVolume 30, Issue 12, 15 JunePages —, https: Thus, its error-removal model is not applicable to RNA-Seq data. Oxford University Press is a department of the University of Oxford. We then confined our analysis to assemblies that overlapped with annotated genes.

Our analyses generated a successive reduction in the number of assemblies. In many cases, we saw virtually no overlap between the submaximal and maximal transcripts, indicating that the assemblers produced non-overlapping fragments of the same isoform. L assembly is the length of the assembled transcript, counting only the portion that aligned to the genome, while L annotation is the length of the annotated transcript.

However, in practice, the overlap between the assembled and annotated transcript is almost always perfect Fig.

Bvi of contigs to scaffolds also differs in genome and transcriptome assembly. On top of this, we added modifications of our own, suitable for transcriptome studies. The proposed pipeline consists of six modules in total. This, ggi, is inappropriate for transcriptome assembly because of alternative splicing and variable gene expression levels.

All assemblies were processed with 10 threads, on a computer with two Quad-core Intel 2. One might naively attribute the differences in transcript numbers to alternative splice forms, but we would advise caution. Finally, SOAPdenovo-Trans, unlike Trinity and Oases, does not yet perform strand-specific assembly, and this is planned for a future development to further improve this algorithm.


In ngi case of the rice transcriptome, about Trinity introduced a new error removal model to account for variations in gene expression levels and then used a dynamic programming procedure to traverse their graphs.

Genome-wide association study identifies two risk loci for tuberculosis in Han Chinese.

To carry out these types of analyses requires an assembler that can reconstruct the transcripts from very short reads e. Hence, the two sequences almost always represent the same isoform. However, there is a lot of room for improvement, e.

The L dataset contained Current multiple k -mers assembly strategies generally fall into one of the two categories: Overlaps between the assembly and annotation. For Permissions, please e-mail: These programs were big to recover sequences for genomes of a known estimated size with a defined number of chromosomes.

Ideally, we should have used japonica transcriptome data, but we used indica transcriptome data instead because there is little japonica data from the Illumina platform ngi is freely available. In instances where multiple consensus sequences were assembled, we selected the sequence that had a length most consistent with the gap size.

Furthermore, we expected that, given no extensive assembly errors i. Sign In or Create an Account. Articles by Jingying Huang.

Email alerts New issue alert. These results suggest that, perhaps, there is information in these datasets that, with additional algorithm modifications, can be recovered. These cannot be corrected by global error removal.

Because multiple assemblies could align to the same genome locus, we generated two datasets: