Assembly Settings

_images/AssemblySettings.png

Mode [1] (Required)

Choose an assembly mode.

Note

  • Conservative: Conservative mode is least likely to produce a complete assembly but has a very low risk of misassembly.
  • Normal: Normal mode is intermediate regarding both completeness and misassembly risk.
  • Bold: Bold mode is most likely to produce a complete assembly but carries greater risk of misassembly.
  • Default: Normal.

Method [1] (Required)

Choose an assembly method.

Note

  • Long-read-only assembly: Long-read-only assembly using only long reads.
  • Hybrid assembly: Hybrid assembly using both Illumina reads and long reads.
  • Default: Hybrid assembly.
_images/AdvancedAssemblySettings.png

VCF [1] (Optional)

Produce a VCF by mapping the short reads to the final assembly if selected.

Note

  • Default: not selected.

Trimmomatic settings [2]

Trim Illumina reads when it is necessary.

Note

  • Illumina reads will be trimmed in “Assembly” step only when all the following two conditions are satisfied:
    1. Hybrid 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](1, 2, 3) Unicycler https://github.com/rrwick/Unicycler
[2]Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic