ライフサイエンスコーパス: contig

1 o be broken up into many separate sequences (contigs).

2 or whole proteins being encoded on a single contig.

3 ated with assays of markers from a sequenced contig.

4 e were assembled de novo into 138,183 unique contigs.

5 ced BAC and next generation sequencing (NGS) contigs.

6 sembled locations and subsequently scaffolds contigs.

7 ine the correct order and orientation of the contigs.

8 ensitive plants identified 30 candidate NTSR contigs.

9 short overlapping sequence reads into larger contigs.

10 antially higher N50 values for scaffolds and contigs.

11 order to determine the correct order of the contigs.

12 e incomplete and fragmented into hundreds of contigs.

13 encing machines still results in hundreds of contigs.

14 ed all three genomes into only a few hundred contigs.

15 e-strand RNA viruses, were identified in two contigs.

16 variants were assembled into long haplotype contigs.

17 every 187 bp from a total of 6888 unique EST contigs.

18 eads were obtained and assembled into 42,630 contigs.

19 r higher-quality sequences such as assembled contigs.

20 to 36,086 contigs and KEGG pathways to 7,032 contigs.

21 contigs after subtraction of age-associated contigs.

22 ce composition is more reasonable to bin the contigs.

23 hnology, which may also lead to misassembled contigs.

24 RA program (90% homology) resulted in 26,087 contigs.

25 Of the 790 concordant contigs, 37 had an exact match to at least one RNA-Seq r

26 Of these contigs, 67,923 contigs had hits to a set of 25,307 unig

27 sm remained within the same species for most contigs (97%).

28 cise ordering of physical maps and sequenced contigs across the whole-genome using these approaches i

29 ified disease-associated viral bacteriophage contigs after subtraction of age-associated contigs.

30 dant contigs in two ways: (1) BLAST-ing each contig against normal RNA-Seq samples, (2) Checking for

31 BLAST-ing these novel contigs against all publically available sequences confi

32 proposed for matching the de Bruijn graph of contigs against reference genes, to derive 'gene paths'

33 A large number of plasmidome contigs aligned with plasmids of rumen bacteria isolated

34 , we developed [Formula: see text] to adjust contigs among bins based on the output of existing binni

35 xic gene revealed as a gap in the sequencing contig and analyzing a few genes in more detail.

36 We assessed the quality of the assembled contig and found that a minimum of 30X coverage of short

37 imming, quality filtering, error correction, contig and scaffold generation and detection of misassem

38 uality reference genomes for Papilio xuthus (contig and scaffold N50: 492 kb, 3.4 Mb) and Papilio mac

39 ld N50: 492 kb, 3.4 Mb) and Papilio machaon (contig and scaffold N50: 81 kb, 1.15 Mb), highly heteroz

40 y identified 75% of extensively misassembled contigs and 100% of locally misassembled contigs in rice

41 in rice, and 77% of extensively misassembled contigs and 80% of locally misassembled contigs in budge

42 (based on a genome size of 606 Mbp), 221 640 contigs and a GC content of 37%.

43 e assembled, de novo, a set of high-fidelity contigs and a sequence scaffold, representing a mean 98%

44 een 31% and 100% of extensively misassembled contigs and between 57% and 73% of locally misassembled

45 ing assemblies through tools for scaffolding contigs and close gaps.

46 d in the generation of various quantities of contigs and functional annotations within the selection

47 es of six tissues were assembled into 18 871 contigs and genome-wide gene expression profiles in tiss

48 blies derived from both traditional sequence contigs and Hi-C pseudomolecules.

49 er to customize the organization of multiple contigs and incorporate knowledge from additional source

50 assigned GO (Gene Ontology) terms to 36,086 contigs and KEGG pathways to 7,032 contigs.

51 ct more than 54% of extensively misassembled contigs and more than 60% of locally misassembled contig

52 Using both the assembled contigs and original long reads as input, BIGMAC first b

53 or example, raw long-read sequencing data or contigs and scaffolds coming from plant genome projects.

54 nGraph was able to substantially improve the contigs and scaffolds from several assemblers.

55 We rigorously assessed the quality of contigs and scaffolds using Illumina mate-pair libraries

56 ysis of the overlap graph and then merged to contigs and scaffolds using mate-pair information.

57 atistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig

58 effectively obtain longer and more accurate contigs and scaffolds.

59 , as indicated by the large number of unique contigs and the lack of a completely assembled genome fo

60 nce in affinity between the higher abundance contigs and the randomly chosen aptamers was observed, s

61 in the loss of unique contiguous sequences (contigs) and relevant biological information.

62 reads (transfrags), genomic sequences (e.g. contigs) and the RNA reads themselves.

63 cted a bacterial artificial chromosome (BAC) contig, and obtained a continuous genomic sequence of 87

64 produce a diagnostic quality score for each contig, and these contig scores are integrated to evalua

65 ion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all

66 he sequence accuracy of the MinION long-read contigs ( approximately 98%) was improved using Illumina

67 gions without the true genome regions in the contigs are corrected with their repeats, this approach

68 found that approximately 13.5% of the final contigs are derived from novel transcribed regions, both

69 We show that the resulting assembled contigs are far larger than in any previous assembly, wi

70 Contigs are functionally annotated based on similarity t

71 Approximately half of the viral contigs are grouped into genetically distinct quasi-spec

72 The resulting contigs are highly accurate and contiguous, while coveri

73 computationally demanding and the assembled contigs are often fragmented, resulting in the identific

74 These contigs are part of a comprehensive transcriptome datase

75 In our implementation, preassembled NGS contigs are used to derive the compact representation of

76 mic Database hierarchy to assign taxonomy to contigs assembled from environmental sequence informatio

77 Large contigs assembled from short HPV reads were obtained fro

78 Random Forests and a dataset of 17,676 viral contigs assembled from shotgun sequencing reads of VLP D

79 During this stage, contigs assembled from the paired-end reads are merged i

80 Following contig assembly into genome-length cDNA, transfected ful

81 Quality filtering and contig assembly resulted in 20,846 unique sequences.

82 se short reads against reference genomes for contig assembly.

83 s by the presence of a repeat, it breaks the contig at the repeat boundaries.

84 era outbreak strain into two nearly finished contigs at >99.9% accuracy.

85 long reads as input, BIGMAC first breaks the contigs at potentially mis-assembled locations and subse

86 Using primers specific for each viral contig, at least one fungal isolate was identified that

87 m the domain regions and assembles them into contigs based on a supervised graph construction algorit

88 contigs based on the plant databases and 45 contigs based on functional domains referencing to the P

89 We annotated 52,725 contigs based on the plant databases and 45 contigs base

90 -cell assembler, SPAdes, in combination with contig binning methods, allowed the reconstruction of ge

91 In metagenomic contig binning, Hetero-RP automatically weighs abundance

92 esulting in markedly improved performance of contig binning.

93 la: see text] can be applied to any existing contig-binning tools for single metagenomic samples to o

94 The genome assembly remains on many contigs, but gene space is estimated to be mostly comple

95 as an increase of the N50 of the extendable contigs by 89.9-94.5% and 80.3-165.8%, respectively.

96 The phylogenetic analysis of these contigs by MG-RAST revealed predominance of Bacteroidete

97 sequencing, de novo assembly, and joining of contigs by Sanger sequencing.

98 Finally, it merges contigs by unused reads.

99 tome containing several tens of thousands of contigs can be annotated in a few minutes of interactive

100 n more local errors can be detected and more contigs can be oriented.

101 coli genome from raw reads yielded a single contig comprising 99.9% of the genome at 98.6% consensus

102 rive 'gene paths' in the graph (sequences of contigs containing gene fragments) that have the highest

103 g-read sequencing platforms have much higher contig continuity and genome completeness as long fragme

104 We propose that these contigs correspond to linear single-stranded DNA molecul

105 After assembly, 478 well-determined contigs could be identified, which are inferred to corre

106 The resulting assembled contigs could be used to identify molecular interactions

107 rial artificial chromosome (BAC) inserts and contigs derived from a low coverage next-generation geno

108 rial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array,

109 to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome.

110 The majority (77%) of analyzed contigs encode transporters with unresolved phylogenies,

111 Five contigs encoding homologs of the catalytic subunit of al

112 A total of 2597 contigs encoding putative CAZymes were identified by CAZ

113 BAC contigs encompass a 1.5-Mb genomic region with 1 Mb of s

114 of contig location can lead to misassembled contigs, even when commonly used quality indicators such

115 A total of 12,299 SNPs, representing 6525 contigs, fit the selected criterion of >/= 60 bp sequenc

116 ing and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequenc

117 The collective contigs for each strain were annotated using the fully a

118 We obtained 126,037, 140,218 and 114,753 contigs for R. bungei, R. cantoniensis and R. brotherusi

119 ses can be used to predict viruses and viral contigs for specific bacterial hosts.

120 A total of 1.07 Mb was recovered in seven contigs for this member of TM6 (JCVI TM6SC1), estimated

121 goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation,

122 ith 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samp

123 nd the other derived from binned metagenomic contigs from an in situ-enriched cellulolytic, thermophi

124 ion from RNA-seq reads and the clustering of contigs from de novo assembled transcriptomes into biolo

125 les to illustrate its utility in identifying contigs from reads that do not map to the genome referen

126 inning tools available, we do not try to bin contigs from scratch.

127 irst tool that can extract complete circular contigs from sequence data of isolate microbial genomes,

128 udies must undergo preprocessing to assemble contigs from sequence data; identify targeted, enriched

129 ocks to reduce assembly gaps caused by small contigs from the input assembly.

130 when only using host genomes or metagenomic contigs from the same habitat or samples as the query vi

131 HALC aligns the long reads to short read contigs from the same species with a relatively low iden

132 accharomyces cerevisiae, assisted by genomic contigs from the same species, BRANCH improved the sensi

133 eads (from Roche 454 chemistry) or assembled contigs (from any sequencing chemistry, including Illumi

134 The number of contigs generated was 53,854 with maximum and minimum le

135 a MiSeq, use read pairing information during contig generation and includes several improvements to r

136 It then constructs a contig graph and, for each long read, references the oth

137 ich efficiently detects bubble structures in contig graphs using graph decomposition.

138 7,060 bp, with a G+C content of 37.2% in 126 contigs (>/= 500 bp).

139 Of these contigs, 67,923 contigs had hits to a set of 25,307 unigenes, including

140 that approximately one-half of the assembled contigs identified homologous sequences in Arabidopsis (

141 Mapping back the reads on the MIRA contigs identified polymorphisms at nucleotide level, us

142 quencing run of bacterial data into a single contig in a few minutes, and assemble 45-fold Caenorhabd

143 are provided to help the user identify which contigs in a genome assembly contain gene targets and to

144 gs and more than 60% of locally misassembled contigs in assemblies of F.tularensis and between 31% an

145 between 57% and 73% of locally misassembled contigs in assemblies of loblolly pine.

146 bled contigs and 80% of locally misassembled contigs in budgerigar.

147 single nucleotide polymorphisms from 27,243 contigs in expressed genomic regions.

148 commended filters for the detection of viral contigs in metagenomic samples ( approximately 6 h), and

149 ethod for the identification of the hosts of contigs in metagenomic studies.

150 led contigs and 100% of locally misassembled contigs in rice, and 77% of extensively misassembled con

151 ring recombination rates, to mapping missing contigs in the human genome.

152 ) mapping, will aid precise anchoring of BAC contigs in the large regions of suppressed recombination

153 dentified non-T4-like viruses and 30% of the contigs in the study potentially infect Synechococcus.

154 nce of functional elements in the concordant contigs in two ways: (1) BLAST-ing each contig against n

155 dict the positions of 65 previously unplaced contigs, in agreement with alternative methods in 26/31

156 netic analyses of the RdRps encoded in these contigs indicate that the putative archaeal viruses form

157 roduces only genome fragments, also known as contigs, instead of an entire genome, it is crucial to g

158 their taxonomic structure, binning assembled contigs into discrete clusters is critical.

159 s multiple samples, to automatically cluster contigs into genomes.

160 acBio) reads or jumping libraries to connect contigs into larger scaffolds or help assemblers resolve

161 Current algorithms can bin contigs into metagenome-assembled genomes but are unable

162 ACOLA, a general framework automatically bin contigs into OTUs based on sequence composition and cove

163 es to resolve individual reads and assembled contigs into species- and strain-level bins.

164 dicators such as read mapping suggest that a contig is well assembled.

165 One of these contigs is approximately 5,600 nucleotides in length and

166 le-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparat

167 pture and sequencing to de novo assembly and contig joining.

168 affolds are fully correct, and >95% of local contig joins are correct.

169 led us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel wit

170 C. elegans genome containing 48 contigs (N50 contig length = 3.99 Mb) covering >99% of the 100,286,40

171 our assembly features a 52-fold increase in contig length and notable improvements in the assembly o

172 Overall reduced sequence contig length is the major problem that challenges the u

173 ance, phylogenetic affiliation and assembled contig length.

174 ension of contigs without prior knowledge of contig location can lead to misassembled contigs, even w

175 Each yielded contigs longer than 100 kb, phase blocks longer than 2.5

176 ering 95% of the reference genome (excluding contigs <200 bp in length).

177 Moreover, EPGA2 parallels the step of Contigs Merging and adds Errors Correction in its pipeli

178 that is highly contiguous and accurate: The contig N50 length is more than ten times greater than an

179 We describe the assembly of its genome to a contig N50 of 2.5 MB.

180 A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb.

181 nerated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44

182 gs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length)

183 racy of the resulting read-overlap graph and contig N50.

184 and generate a de novo assembly of 2.93 Gb (contig N50: 8.3 Mb, scaffold N50: 22.0 Mb, including 39.

185 us wild-type C. elegans genome containing 48 contigs (N50 contig length = 3.99 Mb) covering >99% of t

186 ity using summary statistics (e.g. number of contigs, N50) and in silico evaluation tools.

187 Oxford Nanopore technologies and achieves a contig NG50 of >21 Mbp on both human and Drosophila mela

188 Analysis of the contigs obtained from assembling the unmapped reads pool

189 that comprise multiple operons, including 22 contigs of >1 Mbp.

190 For instance, 28.7-62.3% of the contigs of Arabidopsis thaliana and human could be exten

191 at our method can predict the hosts of viral contigs of length at least 1kbps in metagenomic studies

192 ccurately measures the dissimilarity between contigs of metagenomic reads and that relative sequence

193 novo assembly of the ARV reads generated 19 contigs of two different ARV variant strains according t

194 i.e. the process of ordering and orientating contigs) of de novo assemblies usually represents the fi

195 transcriptome consists of 37 341 transcript-contigs, of which 7% showed significantly different expr

196 We de novo assembled more than 60 000 contigs, of which we found 170 to be regulated dose-depe

197 mbly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisti

198 ing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footpri

199 for extending and joining de novo-assembled contigs or scaffolds guided by closely related reference

200 Based on the accordance graph, the contigs or scaffolds of the target assembly can be exten

201 ligns paired-end (PE) reads and preassembled contigs or scaffolds to a close reference.

202 , followed by the identification of pairs of contigs or scaffolds whose ends disproportionately co-oc

203 gnment of reads or assembled sequences, e.g. contigs or scaffolds, to discrete taxonomic bins.

204 generated, raw sequences are assembled into contigs or scaffolds.

205 ions of sequence seeds for constructing long contigs or scaffolds.

206 lized suffix tree to identify these frequent contigs (or fraction thereof).

207 end to output fragmented contigs or chimeric contigs, or have high memory footprint.

208 The contig orientation problem, which we formally define as

209 In particular, we describe ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabili

210 equencing coverage is available, or the true contig ploidy is low.

211 The vast majority of these novel contigs possess coding sequences, and we have validated

212 Of the 249 concordant contigs predicted by GlimmerHMM to have functional eleme

213 These extra-referential contigs predominantly contained pentameric repeats, espe

214 We discovered a 3,780-bp contig present in all 10 pools that yielded BLASTx E sco

215 lignment to reference genomes and linkage of contigs provided by paired-end reads, as well as the ens

216 rest-neighbor comparison, and through single-contig refinement by iterative-binning and -assembly of

217 g read region can be aligned to at least one contig region, including its true genome region's repeat

218 te alignment and correct it with the aligned contig regions (long read support based validation appro

219 e off-target background data; align enriched contigs representing conserved loci to one another; and

220 ygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudov

221 ielded a resource (LOLbase) including 92,381 contigs representing potentially active transcripts that

222 ethod that estimates the ploidy of any given contig/scaffold based on its allele proportions.

223 tic quality score for each contig, and these contig scores are integrated to evaluate whole assemblie

224 such collapse is often not ideal, as keeping contigs separate can lead both to improved assembly and

225 rated from metagenomic samples or the set of contig sequences produced by assembling these reads.

226 re differentially expressed out of which 478 contigs showed downregulation in root wood and 2263 cont

227 s approximately 24 h: it doubles the average contig size and annotates over 4,300 gene models.

228 r than in any previous assembly, with an N50 contig size of 486,807 nucleotides.

229 Finally, an N50 contig size of at least 86 Kbp can be achieved with 24 x

230 strategies: in the best example, the median contig size was quintupled relative to high-coverage, se

231 , rarefaction, trinucleotide composition and contig spectrum analyses.

232 ucing the count of duplicative and erroneous contigs (strings of high confidence overlaps) in the del

233 ding its true genome region's repeats in the contigs sufficiently similar to it (similar repeat based

234 re consistently more accurate in identifying contig taxonomy than the lowest common ancestor algorith

235 l NGS datasets achieved significantly better contigs than current approaches.

236 sherSC can provide longer and higher quality contigs than existing tools while maintaining high conco

237 n thus result in 11.4-60.7% longer assembled contigs than the existing algorithms.

238 es are applied to short reads directly or to contigs that are generated using de novo sequence assemb

239 elded 790 novel extra-referential concordant contigs that are observed in more than one sample.

240 ed with the wild form, and almost 50% of the contigs that are polymorphic were brought to fixation by

241 ction of a CA and efforts to identify unique contigs that are present in individual k-mer assemblies

242 g the individual assemblies to identify long contigs that can be merged to the consensus assembly.

243 We recover bacterial contigs that comprise multiple operons, including 22 con

244 Here we examined 482 expressed sequence tag contigs that encode putative membrane transporters in th

245 we report a data set of 27,346 marine virome contigs that includes 44 complete genomes.

246 ly of such data usually results in collapsed contigs that represent a variable number of homoeologous

247 ae hypothesis) and 19 expressed sequence tag contigs that show evidence of endosymbiotic/horizontal g

248 ) of this species and identified the genomic contigs that show fixed sequence differences between the

249 Closer analyses of the most abundant contigs, the top 1000 oligonucleotide fragments, and eve

250 The scheme improves upon initial contigs through contig-to-gene identification by BLAST n

251 ) and in silico restriction maps of sequence contigs to a reference.

252 llowing gene fragments contained in multiple contigs to be connected to form more complete (or intact

253 nd transformation of abundances from axolotl contigs to human genes.

254 We compare the contigs to independently produced optical maps to evalua

255 as a means of anchoring unplaced novel human contigs to the reference genome as well as for detecting

256 scheme improves upon initial contigs through contig-to-gene identification by BLAST nearest-neighbor

257 -marker genetic map, and anchored on the map contigs totaling 4.03 Gb.

258 s iodosulfuron + mesosulfuron confirmed four contigs (two cytochromes P450, one glycosyl-transferase

259 li K-12 MG1655 chromosome in a single 4.6-Mb contig using only nanopore data.

260 followed by measuring dissimilarity between contigs using [Formula: see text].

261 nts ranged from ~8 to 1,582 among individual contigs using a normalized depth of coverage (DOC) among

262 erted and direct repeats-in raw read data or contigs using flexible search parameters.

263 rial genomes often can be assembled in a few contigs using only a single Nextera Mate Pair library of

264 le their raw sequence reads and annotate the contigs using RASTtk.

265 Therefore, we attempted to model contigs using relative k-tuple composition, followed by

266 Further analysis revealed that the contig was composed of two major ORFs.

267 sequence of the in silico-assembled 3,780-bp contig was confirmed by gene amplification of overlappin

268 ion, a bacterial artificial chromosome (BAC) contig was constructed for this region using overlapping

269 Annotation of assembled contigs was performed without a priori assumption of the

270 , the highest abundance contiguous sequence (contig) was only present in 0.8% of sequences even after

271 From the annotated contigs, we assigned GO (Gene Ontology) terms to 36,086

272 The affinities of the higher abundance contigs were compared with aptamers randomly chosen from

273 Contigs were deposited at the pubMLST.org/campylobacter

274 , 9,509,783 bp of assembled sequences in 853 contigs were obtained, with an N50 of 117,886 bp and >20

275 Seventy-two clones corresponding to 22 FPC contigs were sequenced by Illumina MiSeq technology.

276 These disease-associated contigs were statistically linked to specific components

277 showed downregulation in root wood and 2263 contigs were up-regulated.

278 sequencing reads or on assembled nucleotide contigs, which themselves are often very fragmented.

279 sequences allow assemblers to produce longer contigs while using less memory.

280 nces are used as guides to scaffold existing contigs, while simultaneously allowing the gene structur

281 ynteny as a means of confirming and ordering contigs will lead to compounded errors.

282 ing reads and the alignment of the resulting contig with a reference sequence.

283 ed the MiSeq-derived scaffolds from each FPC contig with error-corrected PacBio reads, resulting in 1

284 lms whose draft genome contains 5.1 Mb in 55 contigs with 61.2% GC content and includes a 21-gene ars

285 The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96

286 liable SNV calling and to generate assembled contigs with a good coverage of genome and genes.

287 s of S. latifolia and integrated the genomic contigs with a high-density genetic map.

288 ft transcriptome assembly consists of 33 873 contigs with a mean length of 1242 bp.

289 gh quality reads were assembled into 193,462 contigs with a N50 length of 806 bp.

290 dlea composita are encoded on 1- to 7-kb DNA contigs with an exceptionally high GC content, each cont

291 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases.

292 57 reads from two accessions produced 16,115 contigs with an N50 of 889 bp, over 90% of which has sig

293 enomic data generate a large number of viral contigs with missing host information.

294 agments that can be assembled into haplotype contigs with N50 greater than 7 Mb.

295 Sequence data were assembled de novo, and contigs with predicted amino acid sequence similarities

296 Combining contigs with singletons produced 97,241 transcripts.

297 ed, provided a draft genome of 3.9 Mb in 186 contigs (with the largest 15 comprising 90% of the total

298 ies, as well as to orient and place assembly contigs within chromosomes.

299 Over-extension of contigs without prior knowledge of contig location can l

300 ce proxies to accurately position individual contigs without requiring any sequence overlap.