Staden Package / News: Recent posts

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

Finally I decided enough beta releases and packaged an official version of io_lib 1.11.0. Hence from here on I'll support multiple SRF revisions should it change, but I'm confident it's now at a reasonably stable point.

The changes compared to the last beta release are relatively minor (see the change log for full details) and mostly revolve around support for storing both raw and processed solexa traces in the same SRF file.... read more

Yet another new io_lib beta release made, but I think this should be the last beta release before a real non-beta 1.11.0 is released. I'll do this in a couple weeks unless I receive bug reports or SRF changes.

See https://sourceforge.net/project/shownotes.php?group_id=100316&release_id=571271 for a list of changes since 1.11.0b7.

James

My apologies for doing this so late, but it seems given the number of people still having issues getting either the 32-bit binaries to work on 64-bit systems or compiling from scratch that I really should have done this a year ago.

I've put our current Gap4 build for AMD 64 systems in the 1.7.0 staden file-release area. Technically this build is much newer, but the changes aren't significant given very little time has been spent on Gap4 recently.... read more

The latest 1.11 beta release of io_lib is available. Note that this has a major bug fix over 1.11.0b6 in that the SRF files produced now correctly adhere to v1.3 specification. (A bug in b6 produced corrupted files, albeit ones that the code could still read due to the buf existing in both writer and reader.)

I do not anticipate SRF format changes now, but until the code moves out of beta I will not be providing backwards compatibility if the format did change.... read more

(NB: A previous release of this code is available at Li Heng's MAQ site; maq.sf.net)

"tgap" is an experimental curses based (Unix) sequence viewer. It's a completely new program designed to explore new algorithms for handling the huge scale of data from modern sequencing instruments (Illumina/Solexa, ABI SOLiD, etc).

It's not a robust and finished product, and nor is it likely to remain stable in terms of file formats. For now though it'll probably remain text based as this happens to be fast and easy for development/debugging. My advise would be if you want to experiment with it keep a copy of the source and binary along side your databases you produce. I'm not likely to be keeping binary compatibility between releases until much further down the development process.... read more

Anoter incremental update to the io_lib package; still in beta. See the ChangeLog for information.

Io_lib 1.11 have been undergoing beta releases for a while now, but hopefully it is approaching maturity. (This release mainly sees further speed improvements for SRF I/O.)

The main improvements with 1.11 over 1.10 are related to the new short-read format (SRF) archives and a corresponding upgrade to the ZTR specification. If you're at all interested in ZTR or SRF please do check it out and email me (as time constraints mean I don't get to read the forums here particularly often still).... read more

I'm aware that several people are asking about Gap4's suitability for the newer sequencing technologies. Currently gap4 gets pretty memory hungry and slow when dealing with millions of small fragments, but intrinsically it doesn't have any soon-to-be-reached hard limitations. Also the current (or maybe CVS tree version? Sorry for being vague!) gap4 release does support viewing of 454 and solexa trace data too.... read more

The latest Staden Package release has finally been built. Sorry it's taken so long this time.

For now I have just built the source release (which is basically a CVS checkout) and x86 binaries for Linux and Windows. If there's no major problems I'll build releases for other architectures soon.

James

Various bug fixes to 1.9 and support for 454 SFF archives.

See the release notes (https://sourceforge.net/project/shownotes.php?group_id=100316&release_id=426250) for full information.

Mainly a bug fix update and improved support for SFF files. See the release notes for more information.

Binaries and source for Staden Package 1.6.0 are now available.

I have built binaries for Linux (x86), Linux (IA64), Tru64 (Alpha), Solaris (Sparc), MacOSX (PPC) and Windows (x86).

I'll update the web site with release notes etc soon, but for now they can also be read from the files section:

https://sourceforge.net/project/shownotes.php?release_id=361767

Sorry it's been so long!

James

I've built the latest Staden Package code under MS Windows once more and made a new test release for the forthcoming 1.6.0. Experience shows that the windows version has been the hardest to get bug free, mainly due to all development (and hence testing) being done under Linux. Therefore I've put this release out first.

I'll work on the others soon and after some feedback I hope to make an official tested 1.6.0 release. For now I'll work on updating the documentation as I know this is out of date.... read more

The 1.9.0 release of io_lib has finally been uploaded. Please see the release notes and changelog in the files section to view the full list of changes.

It's getting to that stage where io_lib is well overdue for a major overhaul. Not least is the point that the ZTR format can cope with much more than the core Read structure allows, so I propose that the new format has a totally different Read structure (with backwards compatibility mode perhaps).

It is also very inefficient when reading lots of formats due to the insistance on reading from disk. In-memory decoders would streamline the process immensly.... read more

The gcphrap 'patch' (phrap_extras tar, containing additional files for phrap) has been updated. The only change is that sequences longer than 50Kb are now supported when writing out experiment files.

I've now uploaded prebuilt binaries for MacOS X and Solaris 9 for the Staden Package.

James

I've finished working on the current release of the Staden Package and have uploaded a source tarball for version 1.5.3. Please use the files section to read the release notes.

Over the next few days I will upload more binary distributions. Currently available are ix86-linux, alpha-tru64 and (finally) an updated Microsoft Windows version.

I've packaged up a new version of io_lib, as a separate easy to compile and install (hopefully) version. This is the same as is currently in use in the Staden Package, but it came to my attention that the standalone version was out of date.

The most significant changes are the ability to read confidence values in AB1 files and the addition of a trace_dump (instead of scf_dump) program.

The Sparc Solaris binaries for 1.4 have been added to the file release area. Many thanks to the staff at the Bioinformatics Centre in Imperial College for making these available.

I appreciate that this isn't the latest official release, but it's pretty close and the only major change with 1.4.1 was improved documentation. (If you are interested, you could copy this from another 1.4.1 unix release as the documentation is not platform specific except for unix vs windows.)

I've updated the 1.4.0 release to 1.4.1. The key change is the addition of the documentation and some source changes to make it work (with luck!).

James

I've added the SGI (Irix 6.5) binaries to the 1.4 Staden Package release.

The source .tar.gz for V1.4 has been made available along with binaries for Alpha-Tru64, i386-linux and PPC-MacOSX. I may be able to build sparc-solaris and mips-irix/sgi soon, but currently I am unable to build a MS Windows release due to lack of suitable software and hardware.

Volunteers would be most welcome!

In order to keep easier track of versions between the CVS tree and released tars of source and binaries, I have decided to move away from the date version numbering.

From now on, versions are numbered according to the CVS branch. Eg the new 1.4 would have been known as 2004.0. The next release will be either 1.4.1 or 1.5, regardless of the year it is released in.

Thanks to the SF staff, the latest CVS tree has been uploaded. I will make a source tarball soon and in the coming week I plan to upload binary distributions of the latest version for several (but almost certainly not all) systems.

James