Re: Bug#745847: ITP: perm -- efficient mapping of short reads with periodic spaced seeds
Hello,
On Apr 28, 2014, at 2:32 AM, Andreas Tille <andreas@an3as.eu> wrote:
> [Debian Med list in CC]
> Hi Marc,
>
> On Sun, Apr 27, 2014 at 09:57:23AM +0200, Marc Haber wrote:
>> On Fri, 25 Apr 2014 20:53:01 +0200, Andreas Tille <tille@debian.org>
>> wrote:
>>> Description : efficient mapping of short reads with periodic spaced seeds
>>> PerM is a software package which was designed to perform highly efficient
>>> genome scale alignments for hundreds of millions of short reads produced by
>>> the ABI SOLiD and Illumina sequencing platforms. Today PerM is capable of
>>> providing full sensitivity for alignments within 4 mismatches for 50bp SOLID
>>> reads and 9 mismatches for 100bp Illumina reads.
>>
>> I am sure that you know what this means.
>
> Hmmm, you should not be too sure about this - I'm also struggling with
> these terms a bit but I have at least some feeling about the text which
> was copied by Tim from the website of the project.
>
>> I don't. And even after
>> reading for a third time I don't know whether this package may be
>> useful for someone who will likely never align genome scales (assuming
>> this has something to do with microbiology).
>
> Thanks for this helpfull reality check. :-)
>
> I wonder whether there is some volunteer to enhance this description a
> bit from something which sais people not involved into bioinformatics
> "this is not for you". On the other hand I wonder whether we will be
> really able to deliver descriptions to any of our packages which are
> understandable to any random reader who is not involved into this topic.
This tool looks similar to bowtie, which is a very commonly used short read alignment program, so you might look at its description to see if it is any “better”. There are numerous of these tools available now, and determining the differences between them often requires reading the associated research paper...
cheers
Scott
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