Question: Penalty model of BWA MEM and BOWTIE2?
1
gravatar for John
2.0 years ago by
John180
United States
John180 wrote:

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 written 2.0 years ago by John180
2

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 written 2.0 years ago by Santosh Anand5.0k

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

ADD REPLYlink written 2.0 years ago by John180
1

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

ADD REPLYlink written 2.0 years ago by Titus910
1

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 written 2.0 years ago by John180
1

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 written 2.0 years ago by Titus910
1

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 written 2.0 years ago by WouterDeCoster42k
1

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 written 2.0 years ago by Titus910
1

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 written 2.0 years ago by WouterDeCoster42k
2

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 written 2.0 years ago by Santosh Anand5.0k
1

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 modified 2.0 years ago • written 2.0 years ago by Titus910
1

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 written 2.0 years ago by WouterDeCoster42k

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 written 2.0 years ago by John180
2

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 written 2.0 years ago by Santosh Anand5.0k

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 written 2.0 years ago by pinninti1991reddy30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 972 users visited in the last hour