hello, I have an bacterial genome with an average read length of 100bp, sequenced from Illumina platform. I want to assemble this genome. It would be really nice if you would help me with some queries...
Will SPADES be a usefull assembler for such low read length ?
How can I select an reference genome for this bacterial genome ?
How can I calculate the coverage of the genome ?
With MiSeq data (2x250 or 2x300), probably the best assembly you will get is A5_MiSeq. I believe, though I have not tested, it will do a good job with shorter reads. Its log output is really rich in information, including final assembly average coverage.
SPAdes will do a fine job as well.
A google search on "genome coverage calculator" would lead you to this page...