What are reads and contigs?

In bottom-up sequencing projects, a contig refers to overlapping sequence data (reads); 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.

What are common file formats in a bioinformatics enlist different file formats?

File Formats

• The fasta format.
• The fastq format.
• The sam/bam format.
• The vcf format.
• The gff format.

What is molecular file formats in bioinformatics?

MOLECULAR FILE FORMATS The two mostly used molecular file formats are as follows: PDB File format CHARMm file format 2.

What are scaffolds and contigs?

A scaffold is a portion of the genome sequence reconstructed from end-sequenced whole-genome shotgun clones. A contig is a contiguous length of genomic sequence in which the order of bases is known to a high confidence level.

What is read coverage?

Coverage (or depth) in DNA sequencing is the number of unique reads that include a given nucleotide in the reconstructed sequence. Deep sequencing refers to the general concept of aiming for high number of unique reads of each region of a sequence.

What are data types in bioinformatics?

The classic data of bioinformatics include DNA sequences of genes or full genomes; amino acid sequences of proteins; and three-dimensional structures of proteins, nucleic acids and protein–nucleic acid complexes.

What is biological file format?

Biological sequence formats are a collection of file formats that are used in the biomedical sciences. Most of these formats were developed for use in particular programmes and have subsequently been reused by other programmes. A number of web sites are available which will convert one of these formats to another.

What are reads in sequencing?

Definition. In next-generation sequencing, a read refers to the DNA sequence from one fragment (a small section of DNA).

What is the difference between read depth and coverage?

The term “coverage” in NGS always describes a relation between sequence reads and a reference (e.g. a whole genome or al locus), unlike sequencing depth which describes a total read number (Fig. 1). It is very important to distinguish between them: Coverage in terms of the percentage coverage of a reference by reads.

What are paired end reads?

The term ‘paired ends’ refers to the two ends of the same DNA molecule. So you can sequence one end, then turn it around and sequence the other end. The two sequences you get are ‘paired end reads’.