Quality

This produces, not the consensus sequence itself, but an encoding of the "quality" of the data used to create it. The categories of data and the codes produced are shown in the table. For example 'c' means bad data on one strand is aligned with good data on the other. Contigs can be selected from a file of file names or a list. Output is in staden format.

a

Good Good (in agreement)

b

Good Bad

c

Bad Good

d

Good None

e

None Good

f

Bad Bad

g

Bad None

h

None Bad

i

Good Good (disagree)

j

None None

The contigs for which to calculate a consensus can be a particular "single" contig, "all contigs", or a subset of contigs whose names are stored in a "file" or a "list". If a file or list is selected the browse button will be activated and if it is clicked an appropriate browser will be invoked. If the user selects "single" then the dialogue for choosing the contig and the section to process becomes active.

The routine can write its consensus sequence in "staden" format. The output file can be chosen with the aid of a file browser.