Biostar Beta. Not for public use.
Penalty model of BWA MEM and BOWTIE2?
1
Entering edit mode
17 months ago
Jon • 90
United States

Hi dear one, Where I can get the penalty model of BWA-MEM and bowtie2? I could not find literatures! can anyone help me? Thanks in advance

ADD COMMENTlink
2
Entering edit mode

Searcing for the word "penalty" in the respective manuals gives you all the details

http://bio-bwa.sourceforge.net/bwa.shtml

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

ADD REPLYlink
0
Entering edit mode

thanks, i know them, but i want penalty model to compare them

ADD REPLYlink
1
Entering edit mode
ADD REPLYlink
1
Entering edit mode

Thank you! But In this page, it is only given that about the penalty values! I am intended to compare bowtie2 and bwa-mem so I want to compare the penalty model of both! Is there anything related to how penalty model build?

ADD REPLYlink
1
Entering edit mode

The BWA-MEM algorithm has not been published yet. (bottom of the link http://bio-bwa.sourceforge.net/bwa.shtml you didn't read )

But your question is bad because penalty is penalty, you are looking to alignment algorithm/model maybe ...

ADD REPLYlink
1
Entering edit mode

The BWA-MEM algorithm has not been published yet.

It's published on ArXiv but not in a peer-reviewed journal (and it probably never will).

ADD REPLYlink
1
Entering edit mode

oh didn't know that i told that on their web site information, sorry for the mistake. Do you know why it's not reviewed ?

ADD REPLYlink
1
Entering edit mode

AFAIK it was submitted, and Heng Li did not agree with (unreasonable) reviewers comments and then decided not to proceed.

Also doesn't really matter. You can cite and read the preprint.

ADD REPLYlink
2
Entering edit mode

Is it only me who is surprised that we are discussing whether BWA-mem is published and peer-reviewed or not? It looks absolutely ironical given the usage of BWA-mem in the early years before the explosion in the numbers of different kind of aligners, and not to discount the fact that there are still die-hard fans of BWA-mem (including me).

ADD REPLYlink
1
Entering edit mode

that's not changing my point view about this tools at all , i was just curious about it :) It show once again that publication evaluation system got bad points :)

ADD REPLYlink
1
Entering edit mode

bwa mem and bowtie2 are two tools which have been used extensively in the field. Are you sure your comparison is still necessary? It might, of course, be interesting for your own understanding of the tools.

ADD REPLYlink
0
Entering edit mode

thanks for all your answers and discussions, Even though these two are best tools I just want compare and understand both the tools !

Still my question is,

ex: Are Gap open penalty in bowtie2 and bwa-mem meant to be same (in terms of value)? my guide suggested to have a look at penalty models of both the tools then set (change accordingly) a default parameters for both of them!

I didn't get the answer!

Thanks in advance for the future replies!

ADD REPLYlink
2
Entering edit mode

Are Gap open penalty in bowtie2 and bwa-mem meant to be same (in terms of value)?

Do you compare the ripeness of bananas and oranges by comparing their colors, because both are fruits?

BWA-mem and bowtei2 are different algorithms, and for sure there will be differences in how the gap penalty affects one algorithm vs other. Moreover, gap penalty can be set depending upon context too (and bowtie2 provides more parameters to tweak various penalties). For routine exercises, it is recommended to use the default settings. However, if you have specific needs (like your PI wants that), then please read the manuals and relevant materials first, and ask specific Qs, like: "I want to choose X in bwa vs Y in bowtie in context Z because I thought about A, B and C -- is is justified or what are your views?"

ADD REPLYlink
0
Entering edit mode

Hi, Even I'm looking for a optimal aligner and variant caller for analysing human exome data. I performed alignment with different aligners BWA-mem, Bowtie2, Cushaw3 and Novoalign I don't have a accurate answer to say which one is the best.

Have you tried increasing the gap penality to reduce the gaps ?

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3.1