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Staden 2.0.0b9

Program Name: Staden 2.0.0b9

Published By: Rodger Staden

License Type: Freeware

Date Released: April 13, 2012


Staden 2.0.0b9 v1.0 Instant Download

Staden 2.0.0b9 Desciption:


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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

Staden Package 2.0.0b8:

The latest release of the main Staden Package (comprising gap4, gap5, spin, trev and ancillary tools) has just been uploaded.

This is the first release since 1.7 to run on Microsoft Windows again (tested on Vista and XP) and we've also added imroved support for MacOS X thanks to the wonderful open-source community. In addition to that most of the documentation is complete for Gap5. These factors combined means that 2.0 is close to non-beta at long last - probably the next release.

The source is already available. I'll be uploading precompiled binary distributions for various platforms over the remainder of the week, so if they're not available yet, please check in a few days.

Gap5/tg_index 1.2.11

General changes

* Microsoft Windows version. The code should now compile and run under MinGW/Msys on windows.

* MacOS X updates: improved compilation and fixed a few Mac specific display glitches.

* Various code tidyups - less compiler warnings, more portable for linux variants (eg Centos).

* Removed dependency on samtools. (This also avoids a few samtools related bugs, but hopefully not creating new ones to
replace them.)

* Removed dependency on IncrTcl, IncrTk, IncrWidgets. These can still be used for one part of Gap4 (prefinish GUI) but the
code will build and execute without these now.

Gap5 changes

* In-program help should now be working.

* A Disassemble Readings option has been added to the main Edit menu. (This performs the same task as in Gap4.)

* Tg_index now supports the CAF, fasta and fastq formats. When importing fasta/fastq we just create single-read contigs, so it's simply an easy way of importing consensus sequences or a *few* finishing reads. CAF support will import entire assemblies though. Also improved the CAF exporting code.

* First draft of a Find Read Pairs function (as in Gap4). At present read-pair orientation needs some work still, but the
basic plot and searching is working.

* Internal record numbers are now 64-bit instead of 32-bit, removing the need for reserving sequence record IDs in tg_index (-r option) and allowing for more than 2 billion sequences in a gap5 db.

* Contig editor "tag macros" (from gap4) have been added. Use Shift + function key to define a tag macro and then that
function key to apply it.

* A "readings" list now exists (as in Gap4) which is displayed and can be populated using the contig editor "names" panel. The copying (cut/paste) of read names binding has also changed from left-click+drag to middle-click, now matching Gap4.

* Quality value 100 now has a special meaning for the consensus algorithm, as in Gap4. It forces the base to be considered as
true (as it's only possible via a manual edit).

* More contig editor key bindings: Page up/down (already existed for scrolling in 1Kb) can be modified by Shift, Control or Shift+Control to scroll in 10, 100 and 1000Kb steps; [,] keys for setting base quality to 0 or 100; Shift Up/Down arrow and
Control Up/Down arrow for incrementing/decrementing base qualities by 1 or 10.

* Editor Delete now only works on pad characters unless Control Delete is used, in order to prevent accidental removal of real
data.

* Added contig editor "Save Settings" command.

* Internal changes to the template display and Tk canvas.

* Sped up contig editor when dealing with excessively deep alignments.

* Reading names in the contig editor are now be selected for copy and pasting using the left mouse button.

* Tg_index now has a -q option to limit the number of unpaired reads held in memory (for the "-p" option). This significantly
reduces the memory usage on large data sets, at the expense of longer running times.




License: Freeware | Price: $0.00 | Size: 20.0 MB | Downloads (177)

Platform: Windows


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