[Bioperl-l] Status of assembly modules
florent.angly at gmail.com
Fri Jun 18 01:39:39 EDT 2010
Yes, there have been interesting improvements in the assembly BioPerl
module since v1.6.1. You can find these changes in the development
version of BioPerl at http://github.com/bioperl/. I'll take this
opportunity to introduce people who don't follow the commit messages to
the new features that have been introduced:
First, there is support for more file formats from high-throughput
platforms, including those generated by de novo assembly and comparative
assembly tools, such as:
* Roche 454 GS Assembler, aka Newbler (the ACE-454 variant)
There is support for running a lot more of these tools in Bioperl-run
* Roche 454 GS Assembler, aka Newbler
In terms of writing assembly file, I added the option to write ACE
files, which is quite useful because maybe assembly programs recognize
this format. So now you can read assemblies, modify them as you see fit
and exporting them to other programs by writing the modified assembly in
an ACE file.
The internals of the IO parsers have acquired some granularity as it is
now possible to read/write assembly files entirely, or one contig at a
time. This is terrific to reduce memory usage.
That's about it...
PS/ Josh, you filed bug reports related to several of these issues
http://bugzilla.open-bio.org/show_bug.cgi?id=2483). I am closing the
ones that were not closed yet and thank you for submitting patches.
On 18/06/10 14:00, Joshua Udall wrote:
> Florent -
> I didn't want to ask a direct question on-list to perhaps avoid
> confusion. Were you able to improve/submit a ContigIO to bioperl that
> works with one entry at a time (instead of slurping the entire ace
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