The purpose of this page is to list programs available (both
commercial and noncommercial) that have a direct interaction with the
Staden Package. We reserve the right to decide which programs are
listed here and their inclusion in this list does not imply our
preferences or recommendations.
ATQA was developed by Daniel H. Wagner, Associates, and
provides users with confidence assessments for each basecall
derived from an electrophoretic chromatogram. Confidence scores are
computed by evaluating the quality of the fluorescent trace data.
ATQA assigns four confidence scores to each basecall; the first
three scores separately evaluate the likelihood of substitution,
insertion, and deletion errors. The fourth confidence score
corresponds to the combined probability of an error at the basecall
(i.e., a substitution or insertion error) or in the gap following
the basecall (a deletion error).
At present the Staden Package only uses the combined value.
Cap2 is a sequence assembly engine. Gap4 contains an interface to allow use of
Cap2 for assembly. For use within Gap4 a modified version of Cap2 is required.
This is available from the author.
FakII is a sequence assembly engine. Gap4 contains an interface to allow use of
FakII for assembly. For use within Gap4 a modified version of FakII is
required (now based on FakII v4.2). This is available from the authors.
Phrap is a sequence assembly engine. Gap4 contains an interface to allow use of
Phrap for assembly and reassembly. For use within Gap4 a modified version of
Phrap is required. Details on obtaining this are listed in the
Phrap and Gap4
integration page.
Phred is an ABI base calling program. It produces SCF files and can provide
one confidence value for each base. Gap4 can make use of the Phred confidence
values to compute the most probable consensus sequence and consensus
confidence. Gap4 can then search the consensus confidence for poor quality
locations to speed up editing.
PRIDE is a primer design system which can be used as a plugin module to Gap4.
As such it integrates itself in a very tight fashion, even allowing control of
the join editors based on the location of primers.
STARS (Sequence Typing Analysis and Retrieval System) is an alternative
interface to the Staden Package for sequence assembly and management of
sequence-typing projects (MLST). Sequence typing projects typically involve
the sequencing of the same gene, or gene fragment, many times in order to
determine polymorphisms.
