Provides data about whether nucleotide sequences are paired together and their expected paired distance.
Different sequencing technologies have different relative orientations of reads. Geneious
manages this by allowing each pair of a mate to specify its expected mate distance
separately. For example, if unaligned pairs are:
- Forward/Forward (solid) Then the first mate of the pair will have a positive expected distance to its mate and the second mate will have a negative expected distance.
- Forward/Reverse (Illumina short read kit) Then the both mates in the pair will have positive expected distances
- Reverse/Forward (Illumina long read kit) Then the both mates in the pair will have negative expected distances
- Reverse/Reverse (454 from NCBI) Then the first mate of the pair will have a negative expected distance to its mate and the second mate will have a positive expected distance.
The mate distance is defined as the length of the 2 reads plus the distance between them.
Once sequences are placed in a
SequenceAlignmentDocument
, the expected distance now refers to where a sequence
expects to find its mate. If a sequence is placed in the alignment without reverse-complementing, then its expected distance will remain the same as specified above. If the sequence
is placed in an alignment reverse-complemented, then its expected distance will be negated (postive <-> negative).
So, no matter what the sequencing technology used,
when reads are correctly orientated in the alignment, the left-hand read will have a positive expected distance and the right-hand read will have a negative expected distance.
For example, if aligned pairs are:
- Forward/forward data, where the first mate has a positive expected distance and the second has a negative expected distance when unaligned, if they both align to the forward strand,
then their expected distances remain the same. Alternatively, both could align to the reverse strand, in which case their relative order should change (first mate will be on
the right and second mate will be on the left) so their expected distances get negated.
- Forward/reverse data, where both mates have a positive expected distance when unaligned , if the first aligns to the forward strand and the second aligns to the reverse strand
then the first will have a positive expected distance and the second will get negated to become a negative expected distance. Alternatively if the first aligns to the reverse
strand and the second aligns to the forward strand then their relative order should change and so the first mate will end up with a negative expected distance and the second
a positive expected distance in the alignment
All
SequenceAlignmentDocuments
implements this interface.
A
SequenceListDocument
can optionally implement this interface to provide paired read data.
getMateIndex(int)
returns the index of the mate sequence in the list (if any) and
getMateExpectedDistance(int)
returns the expected distance of the mate.
getImmutablePairedReadManager()
returns an immutable view of the paired properties and also provides additional functionality. See
PairedReadManager
The sequence viewer plugin displays paired reads with a little paired-read icon to the left of their name. For paired reads in an alignment, the sequence viewer
also links them together on the same line as long as the 'Link Paired Reads' setting (under 'Advanced') is on. The sequence viewer also has a color scheme
to color paired reads based on how close they are to their expected distance.