Ngs SearchNgsTags.pdf

From Array Suite Wiki

Search NGS Files For Tags

This module uses the Smith-Waterman algorithm and guarantees to find the best local matches. The function can be used to search the exact locations of adapters on each read.




Select the file format and files to search using the "Add" button and then select a Tag File to use.


  • Thread number - Thread number is the total number of threads to be allocated to the process. The more threads that are allocated, the faster the algorithm will run. By default, this is set to the number of CPUs on the user’s computer. This should not be set to a greater number of CPUs than available, but can be reduced at the user’s discretion.
  • Maximal penalty - The maximal number of mismatches allowed plus the gap penalty if an indel is present in the alignment
  • Mismatch penalty - Penalty for a mismatch in the alignment.
  • Open gap penalty - This is the cost to open a gap.
  • Extend gap penalty - This is the cost to extend a gap.
  • Zip format - Select which format is used in compressing the files (default is "None").
  • Report table options:
    • Report Summary: report the summary level table, with the number of tag (Count) on each read position for each tag and each input NGS file
    • Report Details: report the details at read level, recording the position of tag found in each read and each input NGS file. Notice, the table could be very big if your input NGS files contain many reads.
  • Output name - The user can choose to name the output file.