I am currently working on a de novo large genome assembly. now I want to assess the quality of my reconstructed genome. I saw that there are several suitable programs. Some require as input reads in the format BAM / SAM. For example, there are the software:
- ALE: Assembly Likelihood Evaluator (http://www.ncbi.nlm.nih.gov/pubmed/23303509)
- CGAL: Computing Genome Assembly Likelihoods (http://blogs.biomedcentral.com/bmcblog/2013/01/29/cgal-a-new-metric-for-assessing-genome-assembly-quality/)
this are probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. they are classified as "Sequencing > De novo genome sequencing > Assembly evaluation"
But to have SAM or BAM alignment file I have to mappe my FASTQ file to the reference genome but I'm working on a de novo genome assembly. That's why I don't have a reference genome. And I do not always have an available similar genome already validated that I could use as a reference.
some people talk to get the reads in the format BAM / SAM thanks to an alignment with my newly reconstructed genome (but therefore not validated). Do you think that this is possible? does it help to have a correct validation? or is it too incoherent?