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Used for trimming FASTQ files based on quality.

This is not a complicated program. built in C and using Heng Li's kseq.h convenient macros file.


  • -f or --fastq-file, Input fastq file (this is required)
  • -t or --qual-type, Type of quality values (solexa (CASAVA < 1.3), illumina (CASAVA 1.3 to 1.7), sanger (which is CASAVA >= 1.8)) (also, required)
  • -o or --output-file, Output trimmed fastq file (required)
  • -l or --length-threshold, Threshold to keep a read based on length after trimming. Default 20.
  • -x or --no-fiveprime, Don't do five prime trimming.
  • -n or --trunc-n, Truncate sequences at position of first N.
  • -g or --gzip-output, Output gzipped files.
  • --quiet, Don't print out any trimming information