I am trying to analyse NGS data and I heard that these are the hot tools at the moment (bwa, bowtie2 and Novoalign). Are there other tools that can do the same? Am I supposed to be using all of these tools in the analysis of NGS data to get the maximum scope in the final analysis?
I know there was a study comparing these tools and that they were having missing calls and over calls between them but I was wondering if this is the case, why no one is advising to use them all in the analysis to get the best results!
is there a tool that can combine all these analysis tools together?
Its all depend on what you actually want to do. Objective to objective mappers are different.
I give you metafor to it, do u need all vessels for cooking.
Also check comparison of different mapping tool.
http://merenlab.org/2015/06/23/comparing-different-mapping-software/
what is your sequencing type?
the tools you listed is about mapping. For mapping purpose, there are Tophat, Subread, STAR, Bowtie, kallisto , Hisat. Hisat is newly developed, show better performance.
For combined workflow(analysis) of RNA-seq data, please check"hppRNA—a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples"
should be helpful.
Thank you all for the replies. Yes, I read the article but I was wondering if there was a personal approach to the question. If they all give different variant callings, why don't we use them all at the same time?
one can do it, but one is taking time to optimize entire pipeline and then go for optimal results, I am sure results will be different in each methods, but massive variants will be same and a fraction will differ, but if objective is to work on same variants or only variants which are called by one tool. Question is again What was my research question, I was starting with.
Its like using iPhone, Samsung, or Oneplus One, ultimately all just smart phones, if your objective is solved you go with that pipeline.
We saw in Megen analyses that Bowtie, BWA and CLC are clear winners and one is sticking to with one of these winners based on their personal experiences and expertises.
I thought we could use all the tools and merge the information into a VCF file!
I am trying to get the maximum scope by using all the data available.
I am trying to get the principle cause of the disorder but at the same time looking for modifiers.
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