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for bwa : http://bio-bwa.sourceforge.net/bwa.shtml
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?
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 ...
It's published on ArXiv but not in a peer-reviewed journal (and it probably never will).
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 ?
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.
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).
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 :)
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
thanks, i know them, but i want penalty model to compare them
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.
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!
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?"
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 ?