Gaps contig mapping. Medical search. Frequent questions

This paired-end information was subsequently applied to link contigs into scaffolds using a stepwise approach. (biomedcentral.com)
The full-data assembly, however, is so fragmented that SPAdes wasn't able to link contigs into scaffolds, my guess is due to reads mapping to multiple erroneous contigs. (biostars.org)

Clone-by-clone sequencing strategies are based on the construction of a map for each chromosome before the sequencing, and rely on libraries made from large-insert clones. (wikipedia.org)
Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. (frontiersin.org)
WGP technology is based on generation of short sequence tags from terminal ends of restriction fragments of individual BAC clones, followed by assembly of BAC clones into contigs based on shared regions containing identical sequence tags. (frontiersin.org)
5 clones) that constitute ~95 % of the cumulative length of the map. (biomedcentral.com)
A total of 207 BAC clones containing 155 loci were isolated and arranged into a map of linearly ordered overlapping clones over the proximal part of horse chromosome 21 (ECA21), which corresponds to the proximal half of the short arm of human chromosome 19 (HSA19p) and part of HSA5. (uaeu.ac.ae)
The clones form two contigs - each corresponding to the respective human chromosomes - that are estimated to be separated by a gap of ∼200 kb. (uaeu.ac.ae)
Once the contigs are ordered, the gaps that separate them can be identified and associated to the fragments (clones) that are not sequenced properly in the shotgun sequencing phase. (biomedcentral.com)

Due to their complexity, the plants' genome sequences can't be assembled back into chromosomes using only short reads provided by next-generation- sequencing technologies (NGS), and therefore most plant genome assemblies available that used NGS alone are highly fragmented, contain large numbers of contigs, and genome regions are not finished. (wikipedia.org)
To deal with the sheer number of reads generated by today's high-throughput NGS platforms, many of these new assembly tools utilize "Kmers" (words of length K) and de Bruijn graphs, as the method of choice for generating assembled contiguous sequence fragments (contigs). (nature.com)
Long read or contig sets may include Sanger libraries, error-corrected PacBio reads (raw reads are likely to be too error-prone to be merged) and any other source of contigs. (nature.com)
All reads were mapped onto contigs for scaffold building by utilizing the paired-end information. (biomedcentral.com)
It contains the same tools as the CLC Genomics Workbench, such as mapping of reads to a known reference, de novo assembly, and variant calling. (ethz.ch)
MinION sequencing that produces long-reads can be an excellent tool to overcome the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. (preprints.org)
2008), the single reads are then mapped on the TE junction sequences. (stanford.edu)
The selected reads are used to build the contigs (one for each TE sides). (stanford.edu)
2011), the reads are then mapped as pairs (PE) and/or single reads on the TE concatenated sequence. (stanford.edu)
While most of the mapping tools are successful at mapping reads from organisms that exhibit low polymorphism rates, they do not perform well at mapping reads from highly polymorphic organisms. (stanford.edu)
SHRIMP2 maps short reads to a genome even in the presence of a large amount of polymorphism and handles gaps. (stanford.edu)
After the mapping, the reads from proper pairs ( i.e. , two reads on opposite strands) both overlapping the TE breakpoint are assembled. (stanford.edu)
Both TE detection approaches are based on the mapping of reads on the junctions of the TE insertions. (stanford.edu)
It mapped 5 million paired-end solexa reads on my Mac book pro in an hour. (seqanswers.com)
Sequence reads are assembled as contigs , and the coverage quality of de novo sequence data depends on the size and continuity of the contigs (ie, the number of gaps in the data). (rasalifesciences.com)
A typical technique for ordering the contigs is called scaffolding which uses paired reads. (biomedcentral.com)

Whole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. (frontiersin.org)
In this study, we constructed the first comprehensive physical map of wheat chromosome arm 5DS, thereby exploring its gene space organization and evolution. (biomedcentral.com)
Ordering of 80 contigs along the deletion bins of chromosome arm 5DS revealed small-scale breaks in syntenic blocks. (biomedcentral.com)
Gene Mapping also provides clues about which chromosome contains the gene and precisely where the gene lies on that chromosome. (rasalifesciences.com)
Nevertheless, there might really be a gap in the assembled sequence (e.g. between the contigs part in a supercontig or chromosome assembly) and therefore the default value for --min_coverage is 60 (60 percent of the maximal possible query sequence must be covered on every (partial) contig). (webscipio.org)
The probes have been used for molecular hybridizations (fluorescence in situ hybridization, or FISH) in clinical cytogenetics, Y chromosome mapping, sequencing, gene discovery, and comparative Y chromosome studies between the horse and other equids/ Perssodactyls. (veteriankey.com)
gene is mapped on the wheat chromosome 5B, but, neither obtaining a physical marker nor microdissec-, tion of this chromosomal region gave practical results, [56]. (centrocardiobogota.com)
The longest 'Kasalath' BAC contig was observed on the long arm of chromosome 6, and covered an entire genomic region of the 'Nipponbare' rice with a length of 8.18 Mb. (studiodessuantbone.com)

For whole-genome sequence assembly and finishing, the Optical Mapping System is complementary to existing second- and forthcoming third-generation sequencing technologies, he said, in that it can provide a complete genome scaffold for contig alignment and orientation. (genomeweb.com)
Using OpGen's MapSolver software, contigs generated by sequencers are mapped in silico "so that the contigs can be mapped back to the complete ordered optical map scaffold of DNA, giving researchers the ability to very rapidly orient the sequence data to help accelerate assembly and finishing," he said. (genomeweb.com)
Some intra-scaffold gaps were filled by local software using read-pairs in which one end uniquely mapped to a contig and the other end was located within a gap. (biomedcentral.com)
Which is the final SPAdes output file (contig.fasta or scaffold.fasta) should be used for downstream analyses? (biostars.org)
Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arrays and generate a de novo assembly of 2.93?Gb (contig N50: 8.3?Mb, scaffold N50: 22.0?Mb, including 39.3?Mb N-bases), together with 206?Mb of alternative haplotypes. (pacb.com)

In the current study, we have undertaken construction of a sequence-based physical map of pea to address the challenge in the assembly of these repetitive sequences and overcome the shortcomings of traditional restriction digestion based physical maps. (frontiersin.org)
The sequences to be searched for are limited in length by the --gap_to_close parameter, they must be identical between query and target, and the found hits must result in accepted splice sites for the new intron. (webscipio.org)
There exist programs, such as BLAST and MUMmer, that can quickly align and identify high similarity segments between two sequences, which, when seen in a dot plot, tend to agglomerate along a diagonal but can also be disrupted by gaps or shifted away from the main diagonal due to mismatches between the contig and the reference. (biomedcentral.com)
instead, it assembles the fragments into some long contiguous sequences, called contigs. (biomedcentral.com)
The above-mentioned ab, of repetitive sequences in plant genomes (up to 99%), makes difﬁcult the application of this technique for, mapping individual plant genes [40]. (centrocardiobogota.com)

MeGAMerge contigs are supported by read mapping and contig alignment data, when using synthetically-derived and real metagenomic data, as well as by gene prediction analyses and similarity searches. (nature.com)
The interest is not to analyze a detailed alignment between a contig and the reference genome at the base level, but rather to have a rough estimate of where the contig aligns to the reference genome, specifically, by identifying the starting and ending positions of such a region. (biomedcentral.com)
A forced global alignment between a contig and the reference is not only time consuming but often meaningless. (biomedcentral.com)

NEW YORK (GenomeWeb News) - As OpGen intensifies the commercialization of its optical mapping technology, it is looking to expand its use to larger genomes, including humans, within the next year, its CEO said. (genomeweb.com)
They applied their approach to individual bacteria and the mouse gut genome, as well as demonstrate a method for nanopore sequencing-based methylation binning of metagenomic contigs, associating mobile genetic elements with their host genomes, and identifying misassembled metagenomic contigs. (genomeweb.com)

The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. (frontiersin.org)
Of the 155 markers present in the two contigs, 141 (33 genes and 108 STS) were generated and mapped in this study. (uaeu.ac.ae)
Considering limited representation of the region in the latest version of the horse whole genome sequence EquCab2, the dense map developed in this study will prove useful for the assembly and annotation of the sequence data on ECA21 and will be instrumental in rapid search and isolation of candidate genes for traits mapped to this region. (uaeu.ac.ae)
MeGAMerge consistently outperforms individual assembly methods, producing larger contigs with an increased number of predicted genes, without replication of data. (nature.com)
In the paper, a team led by Broad Institute scientists use their activity-by-contact model, which predicts which enhancers regulate which genes, to create enhancer-gene maps in 131 human cell types and tissues, then apply the maps to analyze fine-mapped genetic variants associated with 72 diseases and complex traits. (genomeweb.com)
Genemapping also called linkage mapping can offer firm evidence that a disease transmitted from parent to child is linked to one or more genes. (rasalifesciences.com)
Hence we at RASA Bioinformatic CRO Lab's genome annotation services can also perform gene mapping annotation to discover genes responsible for a disease or disorder or just to get data sufficient enough as the genetic counselling requirements , etc. (rasalifesciences.com)
For comparison, in the Droso-, phila genome the number of such "gaps" reaches, The Arabidopsis genes are compact, contain se, eral exons (with an average size of 250 bp) separated, by short introns. (centrocardiobogota.com)
Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)

Should I consider K55 final_contigs/final_scaffolds or the contigs/scaffolds fasta file in the main output directory image below? (biostars.org)
As you didn't use mate-pairs (at least, you didn't say you had mate-pair libraries), the contigs.fasta and the scaffolds.fasta should be almost the same. (biostars.org)
Then using QUAST evaluated the remaining_contigs.fasta from AlignGraph. (biostars.org)
paths to genome fasta files (required for Sibelia) col.fasta = references/COL.fasta jkd.fasta = references/JKD6008.fasta rf122.fasta = references/RF122.fasta n315.fasta = references/N315.fasta usa.fasta = usa300_contigs.fasta #synteny blocks scale (optional) .blocks = small #reference to use for scaffold naming (optional) .naming_ref = rf122 or, alternatively, if using HAL as input: .references = miranda,simulans,melanogaster .target = yakuba #HAL alignment input. (softwareheritage.org)

Through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome, a total of 6,124 contigs (covering 45.9%) were generated from Canu, and a total of 2,661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon pipeline. (preprints.org)
RASA Bioinformatic Lab's genome annotation services provides you a closer view on the genomic data analysis in understanding the data along with mapping, annotation and as well as comparative genome analysis of two different strains of same species, understanding its working de novo assembly of the genomic data and furthermore providing de-novo based RNA-Sequence Analysis of the data obtained. (rasalifesciences.com)

The construction of BAC-based physical maps of individual chromosomes reduces the complexity of this allohexaploid genome, enables elucidation of gene space and evolutionary relationships, provides tools for map-based cloning, and serves as a framework for reference sequencing efforts. (biomedcentral.com)
Despite having similar gene order and content, the equine region covered by the contigs appears to be distinctly smaller than the corresponding region in human (3.3 Mb vs. 5.5-6 Mb) because the latter harbors a host of repetitive elements and gene families unique to humans/primates. (uaeu.ac.ae)
Newly created genome-wide maps of more than 6 million enhancer-gene connections and their use in interpreting the functions of disease-related genetic variants are reported in Nature this week . (genomeweb.com)
However, the challenges in genome annotation remain daunting [ 10 ], and the research community can anticipate years of additional work and manual curation to produce a true gene map of high quality. (biomedcentral.com)
One of these tools is gene mapping. (rasalifesciences.com)
mapping of the gene is usually the first step of identification of the gene. (rasalifesciences.com)
Gene mapping is usually the starting point of many important downstream studies. (rasalifesciences.com)
If the gene is spread on several contigs, the minimal score applies to the best-scoring partial hit. (webscipio.org)
By default, the --min_dna_coverage is set to 0 and would thus allow even single amino acids found on contigs to be included in the assembled gene. (webscipio.org)

Dual color fluorescence in situ hybridization on metaphase and interphase chromosomes verified the relative order of some of the BACs and helped to orient them accurately in the contigs. (uaeu.ac.ae)
results can serve as an important argument in favour of the proposal to develop a special program for sequencing the genome chromosomes and for, To estimate the possibility of plant genome mapping using human genome probes, the probes fluorescent in situ hybridization (FISH) of human 18S-28S rDNA (clon 22F9 from the LA-13NCO1 library) was carried out on chromosomes of the spring barleyHordeum vulgareL. (centrocardiobogota.com)
The genome is 31.4Mb in size and comprises 14 chromosomes, the mitochondrial genome, the apicoplast genome, and 29 unplaced contigs. (cdc.gov)

As a result, mutations, such as insertions, inversions, and deletions that may be missed with sequencing technologies can be found with the Optical Mapping System, and, similarly, contig misassemblies can be identified and corrected. (genomeweb.com)
Large contig sizes, coupled with the fewest possible misassemblies, are always considered better. (nature.com)

Recently, the consortium has distributed a working draft assembly of the entire genome that removes redundancies, orients sequence fragments and clearly indicates gaps arising from sequencing and assembly. (biomedcentral.com)

These WGP tags were used to assemble 220,013 BACs into contigs. (frontiersin.org)

Each assembler yields different results (contigs and associated information), with some capable of generating ordered contigs if mate pair libraries are available 2 . (nature.com)

Imagine the case that just two stretches of the query sequence by chance map with more or less mismatches to one of the target contigs, while a long part inbetween these stretches is not found. (webscipio.org)
The default value of 0.3 means, that at least about 30 percent of the query sequence must be found on a single contig (the exact formula for the score is: matches minus mismatches, divided by query length. (webscipio.org)

One of the things that we are doing is developing the algorithms and the computational ability to enable that work to take our single-molecule restriction maps that are created and incorporate those and utilize those for the assembly and the gap closure," he said. (genomeweb.com)
The high-quality physical map constructed in this study paves the way for the assembly of a reference sequence, from which breeding efforts will greatly benefit. (biomedcentral.com)
When a single genome is being sequenced, measuring the quality of the assembly is relatively straightforward, with a minimal number of large contigs being ideal. (nature.com)
We describe numerous global features of the genome and examine the relationship of various genetic maps with the assembly. (biomedcentral.com)
At intermediate stages of genome assembly projects, when a number of contigs have been generated and their validity needs to be verified, it is desirable to align these contigs to a reference genome when it is available. (biomedcentral.com)
This information is very useful in ordering the contigs, facilitating post-assembly analysis such as gap closure and resolving repeats. (biomedcentral.com)
It is a tedious and practically impossible task to visually inspect the dot plot to identify the regions covered by a large number of contigs from sequence assembly projects. (biomedcentral.com)
The assembly fully or partially fills 274 (28.4%) N-gaps in the reference genome GRCh38. (pacb.com)

WGP TM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. (frontiersin.org)
This sequence-based physical map will be useful to assemble the genome sequence of pea. (frontiersin.org)
The --max_assemble_size parameter is useful for assemblies with large contigs, while the --min_dna_coverage parameter might be useful for assemblies with short contigs. (webscipio.org)

Similarly, formerly independent maps, based on cytogenetic banding patterns, meiotic crossovers and radiation hybrids, may be placed within the single consensus sequence. (biomedcentral.com)

Should I consider contigs.fa or scaffolds.fa from SPAdes output for downstream analyses? (biostars.org)

The genome can be mapped as a 253,413 bp circle, but its structure is complicated by a large repeated region that is present in 6 copies. (biomedcentral.com)

Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L. (frontiersin.org)

It has three main components: ortholog db, DNA marker and linkage map db, and plant resource db, where multiple plant resources accumulated by different institutes are integrated. (wikipedia.org)
The region presently contains one mapped marker per 22 kb on average, which represents a major improvement over the previous resolution of one marker per 380 kb obtained through the generation of a dense RH map for this segment. (uaeu.ac.ae)

The average contig size is 0.33 Mbp and the N 50 contig size is 0.62 Mbp. (frontiersin.org)
If an intron would have to be created between two partial hits across two contigs, that exceeds the given size, the two hits cannot appear together as parts of one composed hit. (webscipio.org)

OpGen's Optical Mapping Technology is a method of deciphering a genome's architecture by creating high-resolution, ordered, whole-genome restriction maps from single DNA molecules. (genomeweb.com)
And by analyzing the images … we can put them back together and create a whole genome," or, in essence, a whole-genome restriction map, White said. (genomeweb.com)

All tools (exept for gaps) obey to the -h, --help, -V and --version options as one would expect. (onworks.net)

To enable nanopore sequencing for broad methylation discovery, they generated a training dataset from an assortment of bacterial species and develop a technique that combines the identification and fine mapping of the three forms of methylation into a multi-label classification framework. (genomeweb.com)

WGP is designed based on the use of sequence tags generated by next generation sequencing (NGS) and is a powerful alternative to traditional DNA fingerprinting based physical mapping technologies, and also simultaneously generates a partial genome sequence. (frontiersin.org)

It and BGI, OpGen said, had already used the technology to complete a study based on human genome data to successfully close gaps in existing sequence folds. (genomeweb.com)

Non-random shearing occurs because all organisms have in their DNA sequence regions that are more difficult to be sequenced than others, which in some cases transcends into gaps that are not sequenced at all. (biomedcentral.com)

DNA Coverage is a possibility to define the minimum for the mapping of query sequence to the target (explicitly: hit length divided by intron length). (webscipio.org)

To mitigate these problems, we have designed an algorithmic approach called MetaGenomicAssembly by Merging (MEGAMerge) to recursively utilize a number of different Kmer based assemblies and combine the results into a single, merged contig set ( Figure 1 ). (nature.com)

The physical map of 5DS was comprised of 164 contigs, of which 45 were organized into 21 supercontigs, covering 176 Mb with an N50 value of 2,173 kb. (biomedcentral.com)

Complete Genome Sequence of Rickettsia parkeri Strain Black Gap. (cdc.gov)

Fifty-eight of the contigs were larger than 1 Mb, with the largest contig spanning 6,649 kb. (biomedcentral.com)

W file Reset the default output filename witherrors.gaps -x Don't output .cover files -e Set error-rate cutoff to e (e.g. 0.02 is two percent) dnadiff Run comparative analysis of two sequence sets using nucmer and its associated utilities with recommended parameters. (onworks.net)

For strain typing, an optical map of the isolate of interest can be generated in about 24 hours, compared to the days or weeks that it would take with next-generation sequencing-based methods. (genomeweb.com)
A unique genotype of Rickettsia parkeri, designated R. parkeri strain Black Gap, has thus far been associated exclusively with the North American tick, Dermacentor parumapertus. (cdc.gov)

The work, the study's authors write, "highlights a path to creating a comprehensive map of enhancer regulation in the human genome. (genomeweb.com)

Anatomy11

Organisms1

Chemicals and Drugs7

Analytical, Diagnostic and Therapeutic Techniques and Equipment20

Phenomena and Processes30

Disciplines and Occupations2

Anthropology, Education, Sociology and Social Phenomena1

Information Science5

Link contigs into scaffolds2

Clones7

Reads16

Chromosome8

Scaffold5

Sequences5

Alignment3

Genomes2

Genes9

Fasta4

Novo2

Gene9

Chromosomes3

Misassemblies2

Sequence fragments1

BACs1

Mate pair libraries1

Mismatches2

Assembly8

Assemble3

Similarly1

Downstream1

Large1

Reference1

Marker2

Size2

Restriction2

Tools1

Framework1

Partial1

Data1

Organisms1

Length1

Single1

Physical1

Genome sequence1

Larger1

Comparative1

Strain2

Human1