I need to know how many short-reads are enough to do a valid bacterial genome assembly using Velvet and to perform a good annotation? Is it correct to use only a pair of .fastqs? The second part of the question is how to use assembly Velvet output for the genome annotation? GeneMarks software takes a fasta as input and nothing else.
thank you..............................
Apologies, I realised that you are referring to genome assembly, not transcriptome. The same idea applies, however, in reference to read lengths. Also, programs like Rockhopper and Trinity, which I mentioned above, are designed for transcritome assembly.
For genome assembly methods, including annotation, I would encourage you to read this: https://academic.oup.com/bioinformatics/article/30/19/2709/2422249/Evaluation-and-validation-of-de-novo-and-hybrid
Best of luck
Kevin