Ngs SearchNgsAdapters.pdf

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Search NGS Files For Adapters


The Search NGS Files for Adapters module searches raw data files for adapter sequences specified by the user.

To access this module, please select Analysis | NGS | Preprocess | Search Adapters

NGS Search Adapter Menu.png

Input Data Requirements

Accepted file formats include FASTQ, FASTA, QSEC, SFF and AUTO (AUTO allows the use of any combination of the listed file types).

General Options

NGS SearchNGSAdapters.png

Add files

Add files to menu

  • Add button will add samples by selections
  • Add Folder will add all samples in the selected folder (local project only)
  • Search will find files based on sample registration (server project only)
  • Add list will allow users to add files from a list (even add a grouping file for alignment functions).


In the Adapters section, the user can choose to Search default Illumina adapters or to Use customized tag file (FASTA).


  • Job number: The total number of processes running in parallel.
  • Sampling percentage: The user can select what percentage of reads to use for sampling. Sampling takes a subset of reads (randomly).
  • Search 3'End adapters: Selecting this option will search for known adapters at the 3' end of the reads, using the same method as 3' Adapter stripping. This does not include adapters that have bases to the right of the adapter
  • Search right adapters: Using the Smith-Waterman algorithm, this allows for adapters to be in the "right-middle", or have bases to the right of the adapter.
  • Zip format: Select which format is used in compressing the files (default is "None").
  • Output name: The data can be optionally named using the "Output data name" box.

Output Results

Users will get the adapter report like this:

Image m a q03.png

Sort percentage by descending to find the most common adapters in your files.

Image m a q04.png

Then users can filter the adapters using Filter NGS Files module.



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