Polishing Settings

_images/PolishingSettings.png _images/AdvancedPolishingSettings.png

Polishing times (Required)

Set polishing times.

Note

  • Default: 1.

BUSCO settings (Optional)

Set BUSCO options.

Note

  • Select “I want to use BUSCO for the assessement of genome assembly” if you want to use BUSCO. Default: not selected.
  • Select a lineage dataset. Default: Bacteria.

Trimmomatic settings [1]

Trim Illumina reads when it is necessary.

Note

  • Illumina reads will be trimmed in “Polishing” step only when all the following two conditions are satisfied:
    1. No hybrid assembly or without assembly;
    2. Illumina reads filename contains no “HQ”.
  • Remove Illumina adapters provided in the NexteraPE-PE.fa file (provided). Initially Trimmomatic will look for seed matches (16 bases) allowing maximally 2 mismatches. These seeds will be extended and clipped if in the case of paired end reads a score of 30 is reached (about 50 bases), or in the case of single ended reads a score of 10, (about 17 bases).
  • Remove leading low quality or N bases (below quality 3)
  • Remove trailing low quality or N bases (below quality 3)
  • Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15
  • Drop reads which are less than 40 bases long after these steps
[1]Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic