What is a contig file?

A contig (from contiguous) is a set of overlapping DNA segments that together represent a consensus region of DNA. …

What is a contig quizlet?

Contig. – a set of two or more overlapping DNA fragments that form a contiguous stretch of DNA.

What is contig scaffold?

Contigs are continuous stretches of sequence containing only A, C, G, or T bases without gaps. SMRT Sequencing has all of the necessary performance characteristics – long reads, lack of sequence-context bias, and high accuracy – to generate contiguous genome assemblies with megabase-sized contigs.

What is contig assembly?

Contig assembly refers to the process of assembling many sequence fragments into one long genomic sequence or a few long contigs (Figure 3-1). Consequently, any genome-sequencing project will always involve the sequencing of a large number of sequence fragments.

What is a contig explain how you would determine that two clones in a contig are overlapping?

To generate a complete map, first individual overlapping clones are arranged to produce contiguous regions of a chromosome (called a contig). To determine whether two clones overlap we examine each clone for the presence of sequences of DNA that are unique throughout the genome.

What is contig length?

The contig lengths of assembly B are the same as those of assembly A except for the presence of two additional contigs with lengths of 10 kbp and 5 kbp. The size of assembly B is 305 kbp, the N50 contig length drops to 50 kbp because 80 + 70 + 50 is greater than 50\% of 305, and the L50 contig count is 3 contigs.

What is clone contig?

A clone contig is built up by identifying clones containing overlapping fragments, which are then individually sequenced by the shotgun method.

Which is a characteristic of prokaryotic genomes?

The genome of prokaryotic organisms generally is a circular, double-stranded piece of DNA, multiple copies of which may exist at any time. The length of a genome varies widely, but is generally at least a few million base pairs. A genophore is the DNA of a prokaryote.

What is an unplaced scaffold?

Placed scaffolds: the scaffolds have been placed within a chromosome. Unlocalised scaffolds: although the chromosome within which the scaffold occurs is known, the scaffold’s position or orientation is not known. Unplaced scaffolds: it is not known which chromosome the scaffold belongs to.

What is a contig and what are contigs?

Contigs can thus refer both to overlapping DNA sequence and to overlapping physical segments (fragments) contained in clones depending on the context. In 1980, Staden wrote: In order to make it easier to talk about our data gained by the shotgun method of sequencing we have invented the word “contig”.

What is a unitig in data structure?

A unitig is a special kind of contig. Ideally, it is fully consistent with all the data including reads, overlaps, and mate constraints. In practice, unitigs can only be consistent with most of the data. Conceptually, a unitig is a high-confidence contig.

What are ‘unitigs’ and ‘bubbles’ in a contig?

‘unitigs’ are derived from contigs. Wherever a contig end intersects the middle of another contig, the contig is split. ‘bubbles’ are deprecated and will be removed in the next release. Treat them as contigs for now. ‘unassembled’ contains mostly reads that failed to assemble into a contig.

What is a unitig in microbiology?

In practice, unitigs can only be consistent with most of the data. Conceptually, a unitig is a high-confidence contig. Maximal unitigs should contain either (1) unique sequence up to repeat boundaries, with less than a read-length of repeat on each end, or (2) nearly the full extent of a genomic repeat.