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12
A Compartmentalized Approach to the Assembly of Physical Maps
"... We propose a novel compartmentalized method for the assembly of physical maps from fingerprinted clones. Our assembler exploits the presence of genetic markers at the global level to improve the accuracy of the assembly. Experimental results on the genome of rice and barley demonstrate that the comp ..."
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that the compartmentalized assembler produces significantly more accurate maps, and that it can detect and isolate clones that induce chimeric contigs. I.
A Compartmentalized Approach to the Assembly of Physical Maps
"... We propose a novel compartmentalized method for the assembly of physical maps from fingerprinted clones. Our assembler exploits the presence of genetic markers at the global level to improve the accuracy of the assembly. Experimental results on the genome of rice and barley demonstrate that the comp ..."
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that the compartmentalized assembler produces significantly more accurate maps, and that it can detect and isolate clones that induce chimeric contigs. I.
IDBA-MT: De novo Assembler for Metatranscriptomic Data generated from Next-Generating Sequencing Technology
"... Motivation: High-throughput next-generation sequencing technology provides a great opportunity for analyzing metatranscriptomic data. However, the reads produced by these technologies are short and an assembling step is required to combine the short reads into longer contigs. As there are many repea ..."
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Cited by 2 (1 self)
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repeat patterns in mRNAs from different genomes and the abundance ratio of mRNAs in a sample varies a lot, existing assemblers for genomic data, transcriptomic data and metagenomic data do not work on metatranscriptomic data and produce chimeric contigs, i.e. incorrect contigs formed by merging multiple
Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach
"... Background: The quantity of transcriptome data is rapidly increasing for non-model organisms. As sequencing technology advances, focus shifts towards solving bioinformatic challenges, of which sequence read assembly is the first task. Recent studies have compared the performance of different softwar ..."
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Cited by 3 (0 self)
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ambiguity in the assemblies. This analysis further supported the conservative nature of MIRA and CAP3, which resulted in low proportions of chimeric contigs, but high redundancy. Newbler produced less redundancy, but the proportion of chimeric contigs was higher. Conclusion: Our evaluation of four
A: Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PLoS One 2011
"... A frequent step in metagenomic data analysis comprises the assembly of the sequenced reads. Many assembly tools have been published in the last years targeting data coming from next-generation sequencing (NGS) technologies but these assemblers have not been designed for or tested in multi-genome sce ..."
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Cited by 20 (0 self)
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that even under the simplest compositions the number of chimeric contigs involving different species is noticeable. We further showed that the assembly process reduces the accuracy of the functional classification of the metagenomic data and that these errors can be overcome raising the coverage
RESEARCH ARTICLE Open Access Sequencing of BAC pools by different next generation sequencing platforms and strategies
"... Background: Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mat ..."
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. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79 % of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47 % of the total contig
1 Original paper Pooled Assembly of Marine Metagenomic Data Sets: Enriching Annotation through Chimerism
"... Motivation: Despite advances in high-throughput sequencing, ma-rine metagenomic samples remain largely opaque. A typical sample contains billions of microbial organisms from thousands of genomes, and quadrillions of DNA base pairs. Its derived metagenomic data set underrepresents this complexity by ..."
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help our interpretation of the sample. Results: Here we demonstrate quantitatively how careful assembly of marine metagenomic reads within, but also across, data sets can alleviate this problem. For 10 simulated data sets, each with species complexity modeled on a real counterpart, chimerism remained
A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for NextGeneration Sequencing Data,” PLoS
- Computational Biology
, 2014
"... Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequ ..."
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Cited by 2 (0 self)
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sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
"... Due to the complexity of the protocols and a limited knowledge of the nature of microbial communities, simulating metagenomic sequences plays an important role in testing the performance of existing tools and data analysis methods with metagenomic data. We developed metagenomic read simulators with ..."
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Cited by 10 (0 self)
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. Although the increase in contig length was accompanied by increased chimericity, it resulted in more complete genes and a
ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching
, 2014
"... Motivation: Next-generation high-throughput sequencing (HTS) has become a state-of-the-art technique in genome assembly. Scaffolding is one of the main stages of the assembly pipeline. During this stage contigs assembled from the paired-end reads are merged into bigger chains called scaffolds. Due t ..."
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Motivation: Next-generation high-throughput sequencing (HTS) has become a state-of-the-art technique in genome assembly. Scaffolding is one of the main stages of the assembly pipeline. During this stage contigs assembled from the paired-end reads are merged into bigger chains called scaffolds. Due
Results 1 - 10
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