[Bioperl-l] Status of assembly modules

Florent Angly florent.angly at gmail.com
Fri Jun 18 01:39:39 EDT 2010

Hi Joshua,

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)
     * Maq
     * Sam
     * Bowtie
There is support for running a lot more of these tools in Bioperl-run 
Bio::Tools::Run :
     * Roche 454 GS Assembler, aka Newbler
     * Minimo
     * Maq
     * Samtools
     * Bowtie
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
> file)?

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