AMOS/assembly software needs/wants
This is a list of programs that would be nice to have as part of the
AMOS package or just as general tools for assembly work. If you
wish to write one of these, or if you've already written one, please
contact us to have your software included.
- program to select a set of sequences from a bank based on eid,
iid, or regular expression matching eid. The selection should be
inclusive (select all that match) or exclusive (select all that do not
match) and must retrive all records that refer to the selected objects
(e.g. all libraries and fragments). Note: part of this is already
done by bank-report and select-reads.
- program to select a set of sequences from an AMOS or CA fragment
file based on eid (src in CA), iid (acc in CA), or regular expression
matching eid(src). The selection should be inclusive (select all
that match) or exclusive
(select all that do not match) and must retrive all records that refer
to the selected objects (e.g. all libraries and fragments). Note:
part
of this is already done by filterfrg in AMOS/src/Utils
- program to convert from the "old" .afg format containing explicit
MTP records to the "new" .afg format that transfered this information
into the FRG records.
- documentation tool: a combination of uniformly formatted help
messages for all AMOS programs, combined with a program that
automatically generates a set of websites linking to the relevant
documentation. The programs will be categorized by a series of
pre-defined keywords
- full-fledged shotgun sequence simulator that contains different
models of library construction and sequencing errors (in particular for
simulating 454 sequence data)
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