A Bayesian model provides a means to update a prior hypothesis based on evidence.
As an example, in a Bayesian genotype model we may have a prior hypothesis that our sample genotype matches that from a reference sample with probability q. After accounting for evidence of the sample genotype in the form of sequencing reads which are inconsistent with the reference genotype, our hypothesis is updated such that the probability of the sample genotype matching the reference has been reduced to a value less than q.
A De Bruijn graph of m symbols is a graph representing overlaps between sequences. De Bruijn graphs are used for de novo assembly of short read sequences into a genome.
Deprecated refers to software features that are superseded and should be avoided. Although deprecated features remain in the current version, their use may raise warning messages, and deprecated features may be removed in the future. Features are deprecated—rather than being removed—in order to provide backward compatibility and give programmers who have used the feature time to bring their code into compliance with the new standard.
Hashing refers to the use of subfragments of a particular read to find matching pieces of DNA in a hash table.
k-mer means the size of the fragment used for hashing.
A nybble, sometimes spelled "nibble," is a set of four bits. Since there are eight bits in a byte, a nybble is half of one byte.
An orphan read is the unaligned part of paired reads for which only one read aligned. Identical to shadow read.
A shadow read is the unaligned part of paired reads for which only one read aligned. Identical to orphan read.
A singleton is the aligned part of paired reads for which only one read aligned.
A wrapper script is a script whose main purpose is to call a second function in a computer program with little or no additional computation.