I have a genome assembly pipeline which involves identifying reads which map to contaminants such as bacteria. I eventually remove these reads and re-assemble again. My question is regarding the output of abyss pre and post filtering of these reads. The genome I am currently processing is mostly contaminated with bacteria, below is the scaffold stats of abyss
N N:500 E-size Sum Original 81 54 256349 4619298 Post-filter 7621 2006 1226 1805249
Code I used to run abyss
> abyss-pe k=96 name=novo in='R1.fastq R2.fastq'
Does anyone know why N would increase so drastically? Also, I found this in the documentation for E-size: E-size=sum of the square of the sequence sizes divided by the assembly size, but i'm not sure what the biological interpretation of this value is?
any help would be so appreciated! Thank you.