description_of_contig-length-coverage-id_plot.txt

The accompanying pdf file contains length_coverage_id plots generated by using some of the scripts in this repo.

Individual contigs are colored deepskyblue if Pseudomonas aeruginosa (Pa), red if not Pa.

Minor contamination with Pa or non-Pa contigs leads to clusters of short, low depth contigs that will be removed by setting filters for minimum length and depth in shovill. Examples: Isolates 22, 35,  

Major contamination with Pa contigs from another assembly should raise suscpicion that errors in DNA preperation or sequencing occurred. Examples: 56 57 58 61 62 63 64 65. Upon review, these 8 samples occupied a single lane of a 96 well plate used in the library preperation stage; a pipetting error led to the wrong forward adapter being added to these samples. These samples should therefore be resequenced as they represent a mixed assembly.