The new constraints placed on the orientation of the contigs allows for the placement of highly repeated sequences in the genome. (wikipedia.org)
Genome8
in top-down sequencing projects, contig refers to the overlapping clones that form a physical map of the genome that is used to guide sequencing and assembly. (wikipedia.org)
Since these clones should cover the entire genome/chromosome, it is theoretically possible to assemble a contig of BACs that covers the entire chromosome. (wikipedia.org)
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 applied our computational pipeline 'Rapid Analysis of ChIP-Seq data' (RACS) to ChIP-Seq data that was generated in the model organism Tetrahymena thermophila, an example of an organism with a genome that is available in contigs. (arxiv.org)
Conclusions: Altogether, the computational pipeline presented in this report is an efficient and highly reliable tool to analyze genome-wide ChIP-Seq data generated in model organisms with contig-based genomes. (arxiv.org)
I have called SNPs by read mapping illumina reads to reference genome(assembled contigs/scaffolds). (biostars.org)
Further analysis of G-C content and tetranucleotide frequencies could then be used to eliminate chimeric contigs, leaving me with a draft genome. (seqanswers.com)
Pairwise combinations of contig end primers can be used to PCR the organism's genome. (geniuspapers.net)
Scaffolds5
This gives additional information about the orientation of contigs constructed from these reads and allows for their assembly into scaffolds in a process called scaffolding. (wikipedia.org)
Scaffolds consist of overlapping contigs separated by gaps of known length. (wikipedia.org)
The remaining gaps between the contigs in the scaffolds can then be sequenced by a variety of methods, including PCR amplification followed by sequencing (for smaller gaps) and BAC cloning methods followed by sequencing for larger gaps. (wikipedia.org)
But generally speaking, both programs are building different flavors of de Bruijn Graphs from metagenomic reads to generate contigs/scaffolds. (stackexchange.com)
Sophisticated computer algorithms (assemblers and scaffolders) merge these DNA fragments into contigs, and place these contigs into sequence scaffolds using the paired-end sequences derived from large-insert DNA libraries. (nih.gov)
Chromosome5
Contig can also refer to the overlapping clones that form a physical map of a chromosome when the top-down or hierarchical sequencing strategy is used. (wikipedia.org)
the minimum number of clones that form a contig that covers the entire chromosome comprise the tiling path that is used for sequencing. (wikipedia.org)
A 12-Mb complete coverage BAC contig map in human chromosome 16p13.1-p11.2. (umassmed.edu)
Starting with two cosmids within 3p21.1, D3S92 and D3S93, we have isolated two separate contigs of overlapping cosmids within 3p21.1, by screening a library of 5700 chromosome 3-specific cosmid clones. (elsevierpure.com)
Assembling the reads from such a pair (including, of course, only one copy of the identical sequence) produces a longer contiguous read (contig) of sequenced DNA. (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)
I'm considering how to go about generating contigs from reads. (stackexchange.com)
To retrieve such information, metagenomic analysis assembles the WGS reads into relatively longer contigs. (biomedcentral.com)
Contigs are assembled from the shotgun sequencing reads, and paired-end Hi-C reads are mapped to the assembled contigs to generate raw contact maps, which are then normalized to correct the strong experimental biases. (biomedcentral.com)
FASTA2
Clicking these will produce the contigs in FASTA format. (readthedocs.io)
summary.seqs(fasta=current) Using PD_no_oligos.trim.contigs.fasta as input file for the fasta parameter. (mothur.org)
Fragments3
Contigs can thus refer both to overlapping DNA sequences and to overlapping physical segments (fragments) contained in clones depending on the context. (wikipedia.org)
A sequence contig is a continuous (not contiguous) sequence resulting from the reassembly of the small DNA fragments generated by bottom-up sequencing strategies. (wikipedia.org)
Many different restriction fragments derived from these two contigs were found to be evolutionarily conserved and hybridized to distinct message transcripts. (elsevierpure.com)
Genes4
MeGAMerge consistently outperforms individual assembly methods, producing larger contigs with an increased number of predicted genes, without replication of data. (nature.com)
My understanding is that by blasting against a local reference database containing only cyanobacterial genomes, I could bin my contigs by those which contain any cyanobacterial genes and those which do not. (seqanswers.com)
We have identified five new genes from these two contigs and there is evidence to suggest that several additional genes reside within these cosmid contigs. (elsevierpure.com)
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)
Chromosomes5
Did anybody tried running snpEff with VCF as input file containing with contigs instead of chromosomes? (biostars.org)
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)
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)
This led to the identification of 37 contigs representing 37 chromosomes in N. fowleri. (cdc.gov)
Genomes2
ChIP-Seq generates large quantities of data which can be difficult to process and analyse, particularly for organisms with contig based genomes. (arxiv.org)
Contig-based genomes often have poor annotations for cis-elements, for example enhancers, that are important for gene expression. (arxiv.org)
Contiguous3
A contig (from contiguous) is a set of overlapping DNA segments that together represent a consensus region of DNA. (wikipedia.org)
The gel readings in a contig can be summed to form a contiguous consensus sequence and the length of this sequence is the length of the contig. (wikipedia.org)
Here, a contig still refers to any contiguous stretch of sequence data created by read overlap. (wikipedia.org)
Mapping4
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)
Contig Mapping" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (umassmed.edu)
This graph shows the total number of publications written about "Contig Mapping" by people in this website by year, and whether "Contig Mapping" was a major or minor topic of these publications. (umassmed.edu)
Below are the most recent publications written about "Contig Mapping" by people in Profiles. (umassmed.edu)
BACs1
In addition, we have established a 1200-kb sequence-ready contig consisting of 26 cosmids, eight BACs, and eight PACS that encompass this region. (ox.ac.uk)
Scaffold3
Gaps often remain, and a scaffold-consisting of contigs and gaps-that covers the map region is often the first result. (wikipedia.org)
I have VCF file with SNP predicted for each contig/scaffold. (biostars.org)
How can I find a new gene in contig sequences on NCBI? (researchgate.net)
I don't need long stretches of sequence to align, just the presence of a single gene with a good match in a whole contig would be enough to put it in the 'keep' pile. (seqanswers.com)
This article describes how to setup COGs on your system, and how to annotate your gene calls in an anvi'o contigs database with COGs. (merenlab.org)
94 function calls from 2 sources for 47 unique gene calls has been added to the contigs database. (merenlab.org)
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)
Gaps2
The gaps between contigs can be closed by various methods outlined below. (wikipedia.org)
When presented with the sequence contigs I was taught that to fill in physical gaps between contigs we can use PCR. (geniuspapers.net)
Shotgun1
The latter generates contigs, the former generates (some) merged shotgun library inserts. (stackexchange.com)
Assembly2
The assembly of a contig map involves several steps. (wikipedia.org)
In November 2019 46,111 contigs were suppressed because they were contaminants, and the assembly was updated to Turkey_5.1 (GCA_000146605.4). (nih.gov)
Abundance2
I'm assembling RNA-Seq data from 6 related taxa in the basal eudicots and doing some statistical analysis on the abundance profiles of the resulting contigs (EdgeR, WGCNA, etc). (seqanswers.com)
My question for you, the seqanswers community, is what steps (if any) do you take to filter out potentially bad contigs from your trinity assemblies before moving on to abundance estimation and differential expression analysis? (seqanswers.com)
Pipeline1
Will this pipeline accept contig lengths? (biostars.org)
Generate1
Dear all, I am using mauve contig mover through command line .I have a question: once i am running mauve contig mover i am getting n number iteration for each run and for each run mauve generate one folder name alignment1, alignment2. (biostars.org)
Eliminate1
Folks in my lab are kicking around ideas on what procedures to undertake to eliminate trinity contigs that are likely to be false isoforms or replicates within the data set. (seqanswers.com)
Assemblies1
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)
Orientation1
Orientation of RefSNP sequence to contig sequence. (lu.se)
Clusters1
Detailed restriction maps for these two contigs show that they contain multiple clusters of rare cutting restriction endonuclease sites. (elsevierpure.com)
Annotations1
Just to give a ballpark idea: annotations for about 60,000 amino acid sequences were added into the contigs database in about 5 hours using 50 cores. (merenlab.org)
Data1
Select the isolates for which you wish to export contig data for. (readthedocs.io)
Reference1
I was going along the lines of assembling contigs first and searching within them for matches to the reference. (seqanswers.com)
File3
In order to export contigs where at least half the sequence has been tagged (and also the remaining contigs in a separate file), select '50' in the dropdown box for %untagged. (readthedocs.io)
Contig is a command-line defragmenter that can be used to defragment an existing file, or to create a new file of a specified size and name, optimizing it's placement on the disk. (snapfiles.com)
I ran the same sample through the make.contigs and summary.seqs commands above and when the oligos file is included, of the ~400k processed sequences, the group count is 764, however, when I remove the oligos parameter, the group count matches the number of processed sequences. (mothur.org)
Read2
If one end read has a repetitive sequence, as long as its mate pair is located within a contig, its placement is known. (wikipedia.org)
To reiterate, simple read merging tools will not give you assembled contigs. (stackexchange.com)
Large2
Large contig sizes, coupled with the fewest possible misassemblies, are always considered better. (nature.com)
We've tried digital normalization and eliminating contigs with a large number of frame shifts and are comparing results on the first assembled taxon before moving on to the others. (seqanswers.com)
Methods1
BAC contigs are constructed by aligning BAC regions of known overlap via a variety of methods. (wikipedia.org)
Files1
Our BAM files are not fully "analysis-ready" since GATK recommends that a "base quality recalibration" step is performed ( https://gatk.broadinstitute.org/hc/en-us/articles/360035535912 ). (lu.se)
Position1
Start position of snp on contig, counting from 0. (lu.se)
Results1
Alternatively, it can be accessed following a query by clicking the 'Contigs' button in the Export section at the bottom of the results table. (readthedocs.io)
Match1
The resulting table has two download links for each isolate, one for contigs matching the condition, and one for contigs that don't match. (readthedocs.io)
Specific1
Contig is designed to target specific. (snapfiles.com)
Identification1
Childhood-onset schizophrenia/autistic disorder and t(1;7) reciprocal translocation: identification of a BAC contig spanning the translocation breakpoint at 7q21. (umassmed.edu)
Database1
Annotating an anvi'o contigs database with COGs was published on October 25, 2016 and last modified on October 25, 2016 . (merenlab.org)