I am relatively new in de-novo assembly, so please accommodate my question if it is very basic and appear to be naïve. I a working on MI-seq data 2X150bp of a bacterial strain. I used Valvvt (51kmer) and it gave me contigs which looks like this:
NODE253250length121cov1.338843 TGCCTGCTCTTCTGCTTTTCTACCATGTTATGATGCAGTATGAACGCCCTTGCCAGAAGCTGCTGC NODE253255length105cov1.000000 TGGAAGCCCCACTCTCAGTATTGACGTGCAAGTTCACAGTCTGGTTCCTGCCCCCGCGGT------
I have a reference genome of bacteria too. Now I want to pin point in which sample bacteria is present or not. Based on my literature reading- since genome is small I performed denovo assembly. However how from the above contigs I will found out which one is best and useful and showed that bacterial is present? What parameters should I be using- length of contig or something else to find out which one has to be more useful? If I use blast align pairwise alignment with reference, it takes a while and return an error message Bad Gateway perhaps the contig file is large (69523word). Any suggestion or pointers will be highly appreciable.