ライフサイエンスコーパス: assembler

1 operation of the "compartmentalized shotgun assembler".

2 bler based on these called SGA (String Graph Assembler).

3 ead of complete genes, may be reported by an assembler.

4 e and assembled with DNAStar's SeqMan genome assembler.

5 s use the TGICL tool, Megablast and the CAP3 assembler.

6 ly compared with the performance of the base assembler.

7 v3 license from sourceforge.net/projects/spa-assembler.

8 nst high sequencing error rate than the base assembler.

9 y; and AMOScmp, the first comparative genome assembler.

10 k -mer occurs, which is key in transcriptome assemblers.

11 species may behave like repeats and confuse assemblers.

12 t-resolution capabilities of de Bruijn graph assemblers.

13 cused on pre-processing reads and optimizing assemblers.

14 requires less memory space than most of the assemblers.

15 re the performance of EPGA and other popular assemblers.

16 that IVA outperforms all other virus de novo assemblers.

17 ng time of existing overlap-layout-consensus assemblers.

18 tion, affecting the relative ranking of some assemblers.

19 prove the contigs and scaffolds from several assemblers.

20 d data and assumptions and heuristics of the assemblers.

21 with assembly using off-the-shelf long-read assemblers.

22 http://wgs-assembler.cvs.sourceforge.net/wgs-assembler/

23 of magnitude on large genomes versus Celera Assembler 8.2.

24 In this paper we introduce ITD Assembler, a novel approach that rapidly evaluates all u

25 ll our system the Maryland Super-Read Celera Assembler (abbreviated MaSuRCA and pronounced 'mazurka')

26 all, medium, and large genomes shows that JR-Assembler achieves a better or comparable overall assemb

27 Finally, a simulation study shows that JR-Assembler achieves a superior performance on memory use

28 Transcriptome assemblers aim to reconstruct full-length transcripts fr

29 mory required by traditional de Bruijn graph assemblers, allowing millions of reads to be assembled v

30 ly graphs provided by a conventional de novo assembler and alignments of paired-end reads to assemble

31 he manual pipeline of NCTC based on the HGAP assembler and Circlator.

32 -processing step in combination with any NGS assembler and is freely available at http://bix.ucsd.edu

33 es against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quali

34 n assembly varies enormously among different assemblers and different genomes; and third, that the co

35 sted reference-based assembly using multiple assemblers and modes; gene predictor combining; and func

36 er 2 outperforms other de novo transcriptome assemblers and offers accurate and efficient analysis of

37 produce multiple assemblies using different assemblers and parameters, then select the best one for

38 Sophisticated computer algorithms (assemblers and scaffolders) merge these DNA fragments in

39 nal genomics applications, including de novo assemblers and sequence matching programs for SNP callin

40 Multidomain peptides are one such assembler, and in previous work we have demonstrated the

41 ree different assembly programs (PHRAP, TIGR Assembler, and STROLL) on the DNA fragments used in both

42 Tools and pipelines like the assembler, and the workflow management environments make

43 rrected reads are assembled using the Celera Assembler; and (iii) the assembly is polished using a pr

44 , and the other is the "whole genome shotgun assembler" approach, favored by researchers at Celera Ge

45 incorporation of this method into the Celera Assembler are reported for the D. melanogaster, H. sapie

46 (Phred, a base-caller, and Phrap, a sequence assembler) are applied to assess the quality of each bas

47 be the relative performance of the different assemblers as well as other significant differences in a

48 Current genomic sequence assemblers assume that the input data is derived from a

49 Moreover, most assemblers assume uniform read coverage, condition that

50 pressed Burrows-Wheeler transform, and a new assembler based on these called SGA (String Graph Assemb

51 sible groups, is a key element of the entire assembler, because it permits a simple approach to paral

52 In this study, we present a novel de novo assembler, BinPacker, by modeling the transcriptome asse

53 We also show that most published paired read assemblers calculate incorrect posterior quality scores.

54 used to build a next-generation whole genome assembler called BOA (Berkeley Open Assembler) that will

55 We developed a new de novo assembler called IVA (Iterative Virus Assembler) designe

56 requirements, we propose an extension-based assembler, called JR-Assembler, where J and R stand for

57 trate how the modular nature of this peptide assembler can be designed for biological applications.

58 We show that DNA assembler can rapidly assemble a functional D-xylose uti

59 While various NGS assemblers can use information from several libraries of

60 show for the first time that modern de novo assemblers cannot take advantage of ultra-deep sequencin

61 re implementation, Cortex, the first de novo assembler capable of assembling multiple eukaryotic geno

62 ncing technologies, making it one of the few assemblers capable of handling such mixtures.

63 Phylogenetic clustering showed that all assemblers captured a proportion of the most divergent l

64 Resource-efficient genome assemblers combine both the power of advanced computing

65 oid locus as produced by the original Celera Assembler consensus algorithm.

66 open source code is available at: http://wgs-assembler.cvs.sourceforge.net/wgs-assembler/

67 e novo assembler called IVA (Iterative Virus Assembler) designed specifically for read pairs sequence

68 We present TransComb, a genome-guided assembler developed based on a junction graph, weighted

69 er can be considered as a gap-based sequence assembler, different gap sizes result in an almost const

70 euler, in contrast to the celera assembler, does not mask such repeats but uses them inst

71 Integrating MHAP with the Celera Assembler enabled reference-grade de novo assemblies of

72 named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenov

73 However, in contrast to the Celera assembler, EULER-DB does not mask repeats but uses them

74 text of resequencing, we developed a de novo assembler, fermi, that assembles Illumina short reads in

75 and memory requirements of the Velvet/Oasis assembler for the datasets used in this study by 60-85%

76 MaSuRCA against two of the most widely used assemblers for Illumina data, Allpaths-LG and SOAPdenovo

77 Few de novo assemblers for transposable elements exist, and most hav

78 r method is also flexible to embed different assemblers for various types of target genomes.

79 he aforementioned problems prohibit existing assemblers from getting satisfactory assembly results.

80 The output of a genome assembler generally comprises a collection of contiguous

81 Among women, only machine assemblers had significantly increased ALS mortality (ra

82 The Phusion assembler has assembled the mouse genome from the whole-

83 and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better

84 cently a number of de novo and mapping-based assemblers have been developed to produce high quality d

85 ITD Assembler identified the highest percentage of reported

86 nomes generated by a wide variety of de novo assemblers if a good reference assembly of a closely rel

87 produced by deep sequencing, such as de-novo assemblers, ignore the underlying diversity.

88 n particular, we show that our FragmentGluer assembler improves on Phrap and ARACHNE in assembly of B

89 Most recent assemblers include a scaffolding module; however, users

90 ts in both recall and precision over leading assemblers, including StringTie, Cufflinks, Bayesembler,

91 ient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using compa

92 cells: iron transporter, iron-sulfur cluster assembler, iron-storage protein, antioxidant and stimula

93 ITD Assembler is a very sensitive tool which can detect part

94 Microarray Data Assembler is specifically designed to simplify this task

95 t: first, that data quality, rather than the assembler itself, has a dramatic effect on the quality o

96 e web at http://www.engr.uconn.edu/~htd06001/assembler/leap.zip

97 Available de novo assemblers leave repetitive portions of the genome poorl

98 The choice of reference assembler, mapper and variant caller also significantly

99 nd laboratory technicians and female machine assemblers may be at increased risk of death from ALS, s

100 We developed MULTIDOMAIN ASSEMBLER (MDA) to address the special problems that ari

101 present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembli

102 e of repeat analyses, the Assisted Automated Assembler of Repeat Families algorithm has been develope

103 levels of Survival of Motor Neuron, a master assembler of spliceosomal components.

104 best-characterized function of SMN is as an assembler of spliceosomal small nuclear ribonucleoprotei

105 This complex acts as an "assembler" of [4Fe-4S] clusters; i.e., the two GRX5-dona

106 he SMN complex is the identifier, as well as assembler, of the abundant class of snRNAs in cells beca

107 We tested ITD Assembler on The Cancer Genome Atlas AML dataset as a tr

108 outperforms almost all the existing de novo assemblers on all the tested datasets, and even outperfo

109 tasets, and even outperforms those ab initio assemblers on the real dog dataset.

110 longer, indicating that the advantages of JR-Assembler over current assemblers will increase as the r

111 mpled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted gene

112 compare unigene sets generated by different assemblers: Phrap, Cap3 and Cap4.

113 ine the first complete structures of the key assembler protein, SMN, and the truncated isoform, SMNDe

114 e WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the

115 However, most de novo assemblers require enormous amount of computational reso

116 onnect contigs into larger scaffolds or help assemblers resolve ambiguities in repetitive regions of

117 arameter selection and execution of multiple assemblers, scores the resulting assemblies based on mul

118 Most assemblers select a single assembly according to ad hoc

119 compare assembly quality across a variety of assemblers, sequence data types, and parameter choices.

120 ely available as open-source from http://wgs-assembler.sf.net under the GNU Public License.

121 Using MHAP and the Celera Assembler, single-molecule sequencing can produce de nov

122 Our proposed meta-assembler Slicembler partitions the input data into opti

123 In comparison with three de Bruijn graph assemblers (SOAPdenovo, IDBA-UD and MetaVelvet), Omega p

124 framework is based on a novel short peptide assembler (SPA) that assembles protein sequences from th

125 etagenome." A recently developed single-cell assembler, SPAdes, in combination with contig binning me

126 de novo short-read genome and transcriptome assemblers start by building a representation of the de

127 red to as Scoring-and-Unfolding Trimmed Tree Assembler (SUTTA), and present experimental results on s

128 Existing WGS assemblers take a column-by-column approach to consensus

129 R-DB algorithm that, similarly to the Celera assembler takes advantage of clone-end sequencing by usi

130 e present a new transposable element de novo assembler, Tedna, which assembles a set of transposable

131 , it generated the longest contigs among all assemblers tested.

132 We present a new Eulerian assembler that generates nearly optimal short read assem

133 llop, an accurate reference-based transcript assembler that improves reconstruction of multi-exon and

134 Our DNA sequence assembler that incorporates the data structure is freely

135 hese issues with Canu, a successor of Celera Assembler that is specifically designed for noisy single

136 We present HINGE, an assembler that seeks to achieve optimal repeat resolutio

137 recent development is the implementation of assemblers that are built according to explicit statisti

138 Most state-of-the-art assemblers that can achieve relatively high assembly qua

139 Those assemblers that do report uncertainty take different app

140 graph model of assembly, unlike most de novo assemblers that rely on de Bruijn graphs, and is simply

141 nly known viable path to utilize NGS de novo assemblers that require more memory than that is present

142 e genome assembler called BOA (Berkeley Open Assembler) that will easily scale to mammalian genomes.

143 The state-of-the-art sequence assemblers then construct the whole genomic sequence fro

144 developed a targeted iterative graph routing assembler, TIGRA, which implements a set of novel data a

145 c design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel compu

146 quence assembly was produced using the Atlas assembler to combine whole genome shotgun sequences with

147 munication, SGA provides the first practical assembler to our knowledge for a mammalian-sized genome

148 Meanwhile, BLESS can extend reads like DNA assemblers to correct errors at the end of reads.

149 It is nearly impossible for these DNA assemblers to handle the huge amount of data produced by

150 ved quality of the resulting sequences allow assemblers to produce longer contigs while using less me

151 In contrast, using the popular assembler tool Trinity (r2013-02-25), only 14 transcript

152 Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcript

153 Without special modifications, assemblers tuned for homogeneous sequence data may perfo

154 and methods are freely available, as are all assemblers used in this study.

155 see text] compared to the resource-efficient assemblers using benchmark datasets from GAGE and Assemb

156 sive comparison of JR-Assembler with current assemblers using datasets from small, medium, and large

157 However, many DNA assemblers using overlap graphs suffer from the need for

158 We compare our software to current assemblers using simulated and real data.

159 Many de novo assemblers using the de Bruijn graph of a set of the RNA

160 assembly method, referred to as Viral Genome Assembler (VGA).

161 embly optimization pipeline based on Trinity assembler was developed to obtain a reference Hydration-

162 Celera Assembler was modified for combinations of ABI 3730 and

163 The performance of different assemblers was compared in terms of phylogenetic cluster

164 Omega (overlap-graph metagenome assembler) was developed for assembling and scaffolding

165 ntral processing unit time than most current assemblers when the read length is 150 bp or longer, ind

166 pose an extension-based assembler, called JR-Assembler, where J and R stand for "jumping" extension a

167 troduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of partic

168 Here, we report a new method, DNA assembler, which allows the assembly of an entire bioche

169 g error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OL

170 mplemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/

171 hen assembles the mega-reads using the CABOG assembler, which was designed for long reads.

172 We propose that Scy is a molecular "assembler," which, by sequestering DivIVA, promotes the

173 the advantages of JR-Assembler over current assemblers will increase as the read length increases wi

174 An extensive comparison of JR-Assembler with current assemblers using datasets from sm

175 The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homo

176 de Bruijn graph and overlap-layout-consensus assemblers with a novel partitioned sub-assembly approac

177 mbines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de Bru