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Old 07-08-2008, 04:15 AM
Charles Plessy
 
Default Bug#489836: ITP: maq -- Mapping and Assembly with Quality

Package: wnpp
Severity: wishlist
Owner: Charles Plessy <plessy@debian.org>

Package name : maq
Version : 0.6.7
Upstream Author : Heng Li <lh3@sanger.ac.uk>
URL : http://maq.sourceforge.net/
License : GPL-3
Programming Lang: C
Description : Mapping and Assembly with Quality

Maq builds mapping assemblies from short reads generated by the
next-generation sequencing machines. It is particularly designed for
Illumina-Solexa 1G Genetic Analyzer, and has a preliminary functionality to
handle ABI SOLiD data. Maq is previously known as mapass2.
.
With Maq you can:
o Fast align Illumina/SOLiD reads to the reference genome. With the
default options, one million pairs of reads can be mapped to the
human genome in about 10 CPU hours with less than 1G memory.
o Accurately measure the error probability of the alignment of each
individual read.
o Call the consensus genotypes, including homozygous and heterozygous
polymorphisms, with a Phred probabilistic quality assigned to each base.
o Find short indels with paired end reads.
o Accurately find large scale genomic deletions and translocations with
paired end reads.
o Discover potential CNVs by checking read depth.
o Evaluate the accuracy of raw base qualities from sequencers and help
to check the systematic errors.
.
However, Maq can NOT:
o Do de novo assembly. (Maq can only call the consensus by mapping reads
to a known reference.)
o Map shorts reads against themselves. (Maq can only find complete overlap
between reads.)
o Align capillary reads or 454 reads to the reference. (Maq cannot align
reads longer than 63bp.)


Like velvet and patman, this package is intended to be made available after
Lenny is released.

Preliminary packaging is available here:

Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/

--
Charles Plessy
Debian-Med packaging team.



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Old 07-08-2008, 05:03 AM
"Paul Wise"
 
Default Bug#489836: ITP: maq -- Mapping and Assembly with Quality

On Tue, Jul 8, 2008 at 12:15 PM, Charles Plessy <plessy@debian.org> wrote:

> Description : Mapping and Assembly with Quality

Please add "genetic" to the short description and no need to
capitalise the words. Also, is "with Quality" needed, perhaps it needs
to be "with probabilistic quality"?

--
bye,
pabs

http://wiki.debian.org/PaulWise


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Old 07-08-2008, 05:51 AM
Charles Plessy
 
Default Bug#489836: ITP: maq -- Mapping and Assembly with Quality

Le Tue, Jul 08, 2008 at 01:03:26PM +0800, Paul Wise a écrit :
> On Tue, Jul 8, 2008 at 12:15 PM, Charles Plessy <plessy@debian.org> wrote:
>
> > Description : Mapping and Assembly with Quality
>
> Please add "genetic" to the short description and no need to
> capitalise the words. Also, is "with Quality" needed, perhaps it needs
> to be "with probabilistic quality"?

This short description is actually the expansion of the `Maq' acronym. I
usually like to expand acronyms in the short description, but if it is
not appropriate, I will change it.

The sourceforge description is: "map and assemble fixed-length
Solexa/SOLiD reads in a fast and accurate way", but it is probably too
technical in the "If you can't understand it, you don't need it" way.

How about "builds assembly by mapping short reads to reference
sequences"? (cut from Upsteam's website) The mapping is definitely not
genetic, and if the authors avoided "genomic", there is probably a good
reason for.

Have a nice day,

--
Charles Plessy
Debian-Med packaging team,
Tsurumi, Kanagawa, Japan


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Old 07-08-2008, 06:33 AM
"Paul Wise"
 
Default Bug#489836: ITP: maq -- Mapping and Assembly with Quality

On Tue, Jul 8, 2008 at 1:51 PM, Charles Plessy <plessy@debian.org> wrote:

> This short description is actually the expansion of the `Maq' acronym. I
> usually like to expand acronyms in the short description, but if it is
> not appropriate, I will change it.

Ah. My post was because I was concerned it might be confused with
something to do with creating geographic maps.

The problem boils down to the short description not having any words
that are specific to the field the package relates to. Like saying
that GCC converts byte sequences to other byte sequences

--
bye,
pabs

http://wiki.debian.org/PaulWise


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Old 07-08-2008, 06:56 AM
Charles Plessy
 
Default Bug#489836: ITP: maq -- Mapping and Assembly with Quality

Le Tue, Jul 08, 2008 at 02:33:41PM +0800, Paul Wise a écrit :
>
> The problem boils down to the short description not having any words
> that are specific to the field the package relates to.

I am actually quite happy that the jargon of genomics is still using
common dictionnary words. The downside of this is, as you said, that
unless we add "biological" in the description, there will not be
specific words in the descriptions.

For Lenny, we just removed the `[Biology]' tag that was heading the
short descriptions of the packages maintained by the Debian-Med
packaging team, and my gut feeling was that forcing additions of
"biological" in a field where space is limited was letting the
`[Biology]' tag come return by the backdoor.

The more we signal to non-biologists that the package is not for them,
the less we can tell biologists what it does. Couldn't we rely on
Debtags to indicate the field of the package to our users?

Have a nice day,

--
Charles Plessy
Debian-Med packaging team,
Tsurumi, Kanagawa, Japan


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Old 07-08-2008, 07:15 AM
Andreas Tille
 
Default Bug#489836: ITP: maq -- Mapping and Assembly with Quality

On Tue, 8 Jul 2008, Charles Plessy wrote:


For Lenny, we just removed the `[Biology]' tag that was heading the
short descriptions of the packages maintained by the Debian-Med
packaging team, and my gut feeling was that forcing additions of
"biological" in a field where space is limited was letting the
`[Biology]' tag come return by the backdoor.


I would try to use common sense where to put biological or genetic
or whatever into short description and there should be no principle
to avoid certain words.


The more we signal to non-biologists that the package is not for them,
the less we can tell biologists what it does. Couldn't we rely on
Debtags to indicate the field of the package to our users?


Debtags is fine but we have to many package interfaces that do not
know about Debtags and thus we can not rely on this.

Kind regards

Andreas.

--
http://fam-tille.de


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Old 07-08-2008, 07:16 AM
Raphael Hertzog
 
Default Bug#489836: ITP: maq -- Mapping and Assembly with Quality

On Tue, 08 Jul 2008, Charles Plessy wrote:
> The more we signal to non-biologists that the package is not for them,
> the less we can tell biologists what it does. Couldn't we rely on
> Debtags to indicate the field of the package to our users?

No. Debtags is meant for searching, it's not meant to convey information
directly to the user (even if it obviously does). But the user must be
able to have a good idea of what the package does without looking at
debtags.

Cheers,
--
Raphaël Hertzog

Le best-seller français mis à jour pour Debian Etch :
http://www.ouaza.com/livre/admin-debian/


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Old 07-08-2008, 07:25 AM
Lars Wirzenius
 
Default Bug#489836: ITP: maq -- Mapping and Assembly with Quality

ti, 2008-07-08 kello 14:51 +0900, Charles Plessy kirjoitti:
> How about "builds assembly by mapping short reads to reference
> sequences"?

Speaking as an outsider to both biology and interior decoration, as far
as I can determine that short description could apply equally well to
genetics and IKEA furniture. How about adding the word "genetic"
somewhere in the sentence? (I'd suggest a place, but since I don't know
genetics, I would probably put it in an inappropriate place. I would not
like to suggest the birth of Godzilla.)



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Old 07-08-2008, 07:55 AM
Don Armstrong
 
Default Bug#489836: ITP: maq -- Mapping and Assembly with Quality

On Tue, 08 Jul 2008, Charles Plessy wrote:
> How about "builds assembly by mapping short reads to reference
> sequences"? (cut from Upsteam's website) The mapping is definitely
> not genetic, and if the authors avoided "genomic", there is probably
> a good reason for.

Consider:

"assembles short fixed-legth DNA sequences by mapping to reference sequences"

The reason why they don't mention genomics is because the reference
sequence doesn't have to be a genome; it should also include something like:

"This package is likely to be useful for users working with genetics
or genomic studies in biology who need to assembly DNA sequences from
fixed-length sequencers."


Don Armstrong

--
a friend will help you move
a best friend will help you move bodies
but if you have to move your best friend's body
you're on your own
-- a softer world #242
http://www.asofterworld.com/index.php?id=242

http://www.donarmstrong.com http://rzlab.ucr.edu


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Old 07-08-2008, 10:00 AM
Charles Plessy
 
Default Bug#489836: ITP: maq -- Mapping and Assembly with Quality

Le Tue, Jul 08, 2008 at 12:55:01AM -0700, Don Armstrong a écrit :
> On Tue, 08 Jul 2008, Charles Plessy wrote:
> > How about "builds assembly by mapping short reads to reference
> > sequences"? (cut from Upsteam's website) The mapping is definitely
> > not genetic, and if the authors avoided "genomic", there is probably
> > a good reason for.
>
> Consider:
>
> "assembles short fixed-legth DNA sequences by mapping to reference sequences"

Hi Don,

After quickly browsing the Maq's user manual, I get the feeling that its
main feature is not assembly (in particular, it can not compute de novo
assemblies). Its prime function is mapping, and its advantage compared
to other mapping programs is its extended workflow that facilities such
as polymorphism analysis.

How about "maps short polymorphic reads to reference biological sequences".

For me, "read"(s) is an important keyword that I would like to keep in
the description if we do not use the expansion of the acronym that is
used to name the package.

Have a nice day,

--
Charles Plessy
Debian-Med packaging team,
Tsurumi, Kanagawa, Japan


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