ライフサイエンスコーパス: contig

1 mbled these reads into contiguous sequences (contigs).

2 caffolding greatly depends on the quality of contigs.

3 tant de novo methods only yield rather short contigs.

4 le genetic elements in assembled metagenomic contigs.

5 by mapping sequenced reads to the assembled contigs.

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

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

8 contigs after subtraction of age-associated contigs.

9 ce composition is more reasonable to bin the contigs.

10 hnology, which may also lead to misassembled contigs.

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

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

13 sembled locations and subsequently scaffolds contigs.

14 ine the correct order and orientation of the contigs.

15 edictions have also been added for assembled contigs.

16 rly complete bacterial genomes within single contigs.

17 ee genomes were assembled into four or fewer contigs.

18 the coverage and sequence composition of the contigs.

19 pes together with their abundances from such contigs.

20 gs but also paralogous gene loci in distinct contigs.

21 l haplotype reconstruction from preassembled contigs.

22 he contigs or the taxonomic identity of some contigs.

23 ps to accurately detect and correct chimeric contigs.

24 pseudochromosomes containing 76 contigs (N50 contig = 2.8 Mb).

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

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

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

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

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

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

31 Recruitment to viral contigs allows tracking infection dynamics over time and

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

33 Contig analysis indicated a wide variety of mobile beta-

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

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

36 uce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb.

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

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

39 better metagenome-assembled genomes, longer contigs and better functional annotations when compared

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

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

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

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

44 n of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of

45 irection and order relationships between the contigs and make the sequence assembly results more cont

46 l variation detection, scaffolding assembled contigs and mis-assembly detection.

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

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

49 ntly, most genome assembly projects focus on contigs and scaffolds rather than assembly graphs that p

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

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

52 eral, the reads can either be assembled into contigs and searched against reference databases, or ind

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

54 inkage disequilibrium (LD) maps of sequenced contigs and the utility of LD for ordering, orienting an

55 fine-grained visualisation of the assembled contigs and their enriched annotations.

56 enomes were completely assembled into single contigs and three genomes were assembled into four or fe

57 P, which is the first method to classify the contigs and utilize the vertices and edges to optimize t

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

59 raft transcriptome assembly contained 45,866 contigs, and more than half were similar to sequences at

60 hat generated over 600 million reads, 40,830 contigs, and provided the annotation of 25,298 unique tr

61 oft-clipped/split reads, assembles them into contigs, and re-maps contig intervals to a reference gen

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

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

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

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

66 ion of human 6p21.3 from which three shorter contigs are formed.

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

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

69 re severe in shotgun metagenomics, where the contigs are often short, and the existing tools fail to

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

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

72 trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination wit

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

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

75 se short reads against reference genomes for contig assembly.

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

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

78 Unlike classical clustering problem, contig binning can utilize known relationships among som

79 erior sensitivity and precision of VirBin in contig binning for viral haplotype reconstruction.

80 Metagenomic contig binning is an important computational problem in

81 We developed a novel contig binning method, Semi-supervised Spectral Normaliz

82 However, the current state-of-the-art contig binning methods do not make full use of the addit

83 In this work, we presented VirBin, a new contig binning tool for distinguishing contigs from diff

84 We developed a contig binning tool, VirBin, which clusters contigs into

85 The benchmark results with other contig binning tools demonstrated the superior sensitivi

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

87 ering approach, normalized cut, for improved contig binning.

88 esulting in markedly improved performance of contig binning.

89 competes favorably with other tools on viral contig binning.

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

91 d 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or

92 DTA-SiST first extends contigs by reads that have the longest overlaps with the

93 The detection of chimeric contigs can be carried out either by aligning assembled

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

95 Sequence reads or contigs can be represented as vectors and their 'texture

96 s had a diel expression pattern, with 61% of contigs clustering into modules with statistically signi

97 eotide polymorphism (SNP) markers from these contigs co-segregated with LrAp.

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

99 linical concern, e.g., Klebsiella pneumoniae contigs containing KPC-2 within an ISKpn6-like transposa

100 SRAssembler, that efficiently assembles only contigs containing potential homologs of a gene or prote

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

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

103 d features based on sequence composition and contig coverage cannot effectively distinguish viral hap

104 not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous

105 age disequilibrium with each other the inter-contig distances may be roughly estimated by this method

106 Five nucleotide binding leucine-rich repeat contigs distinguished resistant and susceptible bulks an

107 s (ISs) and DNA repeats, for which only a 20-contig draft assembly was achieved.

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

109 Five contigs encoding homologs of the catalytic subunit of al

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

111 able of consistently recovering large cancer contigs even when underlying cancer genomes are highly r

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

113 ith precision measure, due to the read-based contig extension strategy and the elegant transcripts ex

114 f this sequence is unknown, 387 of the novel contigs fall within 315 distinct protein-coding genes, a

115 We assemble a single contig for each haplotype, align them to the reference,

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

117 DTA-SiST constructs splicing graphs based on contigs for each gene locus.

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

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

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

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

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

123 a new contig binning tool for distinguishing contigs from different viral haplotypes with high sequen

124 mes, which suggests that filtering out small contigs from draft genome assemblies may mitigate the is

125 CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existin

126 Assembled contigs from many samples showed similarity to Anthurium

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

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

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

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

131 blem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a

132 metagenomic research, which aims to cluster contigs from the same genome into the same group.

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

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

135 nd Brahman (indicine) cattle subspecies from contigs generated by the trio binning method.

136 nism to "patch" a higher k-valued graph with contigs generated from a lower k-valued graph.

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

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

139 Of 19,907 assembled viral contigs (>5 kb, mean 15 kb), 97% were found in each samp

140 Many E. huxleyi contigs had a diel expression pattern, with 61% of conti

141 In some cases, the contaminating contigs have been erroneously annotated as containing pr

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

143 were assembled de novo, producing > 190,000 contigs, identifying 18,857 coding sequences (CDS).

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

145 ume that each BGC is encoded within a single contig in the genome assembly, a condition that is viola

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

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

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

149 at nearly all contaminants occurred in small contigs in draft genomes, which suggests that filtering

150 For positioning two contigs in linkage disequilibrium with each other the in

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

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

153 n ORN-9707) represented ~7% of all expressed contigs in SG.

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

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

156 ified genomes contained unique mitochondrial contigs, including 21 complete or near-complete mitochon

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

158 ds, assembles them into contigs, and re-maps contig intervals to a reference genome using an efficien

159 contig binning tool, VirBin, which clusters contigs into different groups so that each group represe

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

161 a new approach to reliably separate plasmid contigs into discrete components using sequence composit

162 mutation at another locus, clustering these contigs into genome-scale haplotypes is still needed.

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

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

165 report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis

166 en provides clues on how to combine multiple contigs into segments encoding long BGCs.

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

168 uality of contigs (vertices), and divide the contigs into three types (True, Uncertain and Misassembl

169 Contigs involved in processes that build up energy store

170 In contrast, contigs involved in processes that released energy store

171 A chimeric contig is contig that has been incorrectly assembled, i.

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

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

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

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

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

177 i (assembly size = 182 Mb; shortest scaffold/contig length needed to cover 50% of the genome [N50] =

178 d haplotype-resolved assemblies with minimum contig length needed to cover 50% of the known genome (N

179 We achieve a N50 contig length of 7.7 million bases (Mb) directly from lo

180 panded the alleles for each gene using 1,991 contig-level genome sequences.

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

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

183 ere BGCs are often scattered through several contigs, making it difficult to reconstruct them.

184 tween contigs, some correct edges connecting contigs may be deleted.

185 (quality value > 40) and highly contiguous (contig N50 > 23 Mbp) with low switch error rates (0.17%)

186 updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contigu

187 uced a contiguous and accurate genome with a contig N50 of >15 megabases (Mb) and concordance of 99.9

188 we present a high-quality reference genome (contig N50 of 15.78 megabases) of the maize small-kernel

189 nome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb.

190 mprising 820.1 Mb of genomic sequence with a contig N50 of 2.3 Mb and containing 36 651 annotated pro

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

192 nal assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb.

193 eference-grade genome of T. wilfordii with a contig N50 of 4.36 Mb.

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

195 The assemblies show a contig N50 of 6.32 Mb and 10.53 Mb for Basmati 334 and D

196 Here, we assemble a high-quality genome (contig N50 of 6.99 Mb) of the apple anther-derived homoz

197 dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform genome-w

198 This new reference genome improves the contig N50 of the previous short-read based buffalo asse

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

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

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

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

203 the level of pseudochromosomes containing 76 contigs (N50 contig = 2.8 Mb).

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

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

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

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

208 S corrected long reads can be assembled into contigs of 13.1-29.8% larger N50 sizes than MECAT.

209 ta show that SRAssembler produces homologous contigs of equivalent quality to whole genome assemblies

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

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

212 nd identified the most expressed classes and contigs of O. rostratus SG and MG.

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

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

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

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

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

218 tilize known relationships among some of the contigs or the taxonomic identity of some contigs.

219 gies are required to span gaps and establish contig order and relative orientation.

220 We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the sp

221 nverted contigs than for identifying correct contig orders.

222 The contig orientation problem, which we formally define as

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

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

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

226 achieved after a process of 'binning' where contigs predicted to originate from the same genome are

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

228 revealed 296,485,284 bp in 125,715 distinct contigs present in the populations of African descent, d

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

230 The genome size was 32.57 Mb, and 14 contigs ranging from 0.35 to 4.58 Mb with an N50 of 2.86

231 r, haplotype assembly programs often produce contigs rather than full genomes.

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

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

234 Selected contigs related to the cell cycle also exhibited signifi

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

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

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

238 annot-link constraints mean that the pair of contigs should be clustered in different groups.

239 Must-link constraints mean that the pair of contigs should be clustered into the same group, while c

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

241 All five RenSeq NB_ARC contigs showed identity with the long arm of wheat chrom

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

243 M13 human cell line, HiCanu achieved an NG50 contig size of 77 Mbp with a per-base consensus accuracy

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

245 ferent haplotype abundance distributions and contig sizes, and also on mock quasispecies sequencing d

246 as the reliable taxonomy assignments of some contigs, SolidBin constructs two types of prior informat

247 evertheless, due to the wrong joints between contigs, some correct edges connecting contigs may be de

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

249 ong-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-ho

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

251 eads that have the longest overlaps with the contigs' terminuses.

252 be less informative for correcting inverted contigs than for identifying correct contig orders.

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

254 that has been incorrectly assembled, i.e. a contig that contains one or more mis-joins.

255 A chimeric contig is contig that has been incorrectly assembled, i.e. a conti

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

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

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

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

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

261 RNA expressed in each tissue and one single contig (the acid tail protein ORN-9707) represented ~7%

262 it is difficult to assemble BGCs in a single contig, the structure of the genome assembly graph often

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

264 ficulty of linking relatively short sequence contigs to form much larger chromosome assemblies.

265 be carried out either by aligning assembled contigs to genome-wide maps (e.g. genetic, physical or o

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

267 We then compared all contigs to one another to identify a set of unique seque

268 caffold graph based on the classification of contigs together with the alignment of edges.

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

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

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

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

273 t of paired reads to evaluate the quality of contigs (vertices), and divide the contigs into three ty

274 Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the

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

276 A total of 8,031 contigs were assembled and assigned to different functio

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

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

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

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

281 in assembly contiguity compared to the input contigs, while preserving low error rates compared to th

282 Of note, we obtained three single-contig, whole-chromosome assemblies of rumen bacteria, t

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

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

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

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

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

288 0.3 Mb nuclear genome was assembled into 202 contigs with an N50 of 2.4 Mb.

289 57 reads from two accessions produced 16,115 contigs with an N50 of 889 bp, over 90% of which has sig

290 d for ~67% of all expressed transcripts with contigs with identity to lipocalins and acid tail protei

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

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

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

294 Combining contigs with singletons produced 97,241 transcripts.

295 n N50 of 2.86 Mb were assembled, including 4 contigs with telomeric sequences on both ends and an add

296 c sequences on both ends and an additional 8 contigs with telomeric sequences on either the 5' or 3'

297 In Amaranthus tuberculatus, several contigs, with combined length of 4.6 Mb and with 147 gen

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

299 ructs a variation graph from the short input contigs without making use of a reference genome.

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