So after hearing from Katherine about some ideas for using Platanus, I tried running the Illumina assembly once more, this time using a kmer length of 20. This seems to have had an effect, as the output contig file went from 21mb in size, to 1.9gb. I’m shuffling files around and haven’t had a chance to actually look at the contents of the file, but I’m at least heartened by the massive size increase. Size = data, right?
D-69-91-148-111:RobertsLab Sean$ ~/Documents/RobertsLab/assembly-stats/build/assembly-stats ~/Documents/RobertsLab/Oly_Out_Contig.fa stats for /Users/Sean/Documents/RobertsLab/Oly_Out_Contig.fa sum = 1633553496, n = 12395459, ave = 131.79, largest = 23341 N50 = 141, n = 2124062 N60 = 115, n = 3463771 N70 = 92, n = 5003872 N80 = 69, n = 7087338 N90 = 61, n = 9624083 N100 = 58, n = 12395459 N_count = 0 Gaps = 0