Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

Applied Biosystems SOLiD 4 System SETS Software User Guide
Glossary
Paired-End Paired-end libraries are standard fragment libraries. Sequence reads
are generated from both ends of the fragment (5’>3’ and 3’>5’).
These reads are paired during sequencing and separated by the same
number of bases (typically 50-200 bases).
The paired-end constraints are as follows:
The distance between the F3 and F5 tags must be within a
prescribed range of distances determined by the insert size and
library preparation.
The tags must map such that F3 comes before F5 reading 5’ >
3’.
The tags must map such that F3 and F5 map to opposite strands
on the reference sequence.
Quality Value Accuracy estimation of colorcalling using metrics similar to phred or
KB Basecaller.
Sequencing Run During a SOLiD 4 System sequencing run, two probe sets are used
to maximize the fraction of mappable beads, read length, and
sequencing throughput. (Mappable beads are beads, amplified with
template, that map to the reference genome.) This protocol must be
used for sequencing 50-bp reads of both mate-paired and fragment
libraries. Unlike terminator-based sequencing, the SOLiD 4 System
does not collect base-sequencing information. Instead, five rounds of
primers (Primers A, B, C, D, and E) are used to sequence template by
ligation of di-base labeled probes. For sequencing of fragment
libraries, the set of primers used is specific to the P1 adaptor.
SOLiD 4 Analyzer The sequencing instrument and its supporting computer cluster.
SOLiD 4 System The SOLiD 4 Analyzer, its instrument control software (ICS), and
ancillary equipment.
Spot A series of panels, each panel with unique numbers for ordering
across spots. When multiple samples are run on a single array, each
array has its own spot. This is shown in the file name format S#. For
example, S1 are files for Spot 1.
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