A single molecule of double-strand DNA
For assembly projects, plasmids are chromosomes
Physical piece of DNA, part of a chromosome
Process of breaking the chromosomes into many fragments
The breaking points are randomly distributed
Process of transforming DNA fragments into one or more chromatograms, and then into reads
Process of assigning DNA letters and qualities as defined by chromatograms
Digital representation of a strand of a DNA fragment
Most of times it is shorter than the fragment
Physical length of the fragment, in base pairs
Usually we know it approximately
Number of letters in the read with high quality
The low quality begin and end of the read are trimmed (discarded)
A number representing the confidence that the base-calling process has when determining the bases in the read
It is an integer positive number, usually between 0 and 90
Process of combining many reads to get one or more contigs that (hopefully) correspond to the real chromosome
Set of reads that overlap mutually, and that can be aligned to form a coherent layout
Sequence defined by the majority of the reads in a contig
The majority rule considers the base quality
Number of reads that report a base pair
It is a property of the base pair
Average of base pair depth through all base pairs
It is a property of the sequencing project
Can be calculated before the project
It can mean two things
Depth of coverage
Breadth of coverage
a.k.a Coverage Depth
It is the same as average depth
Percentage of the base pairs in the genome that has at least depth 1
(Sometimes we increase that threshold to a larger number)