Difference between revisions of "Sickle"

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(Created page with "= Introduction = 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. = Us...")
 
 
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= Usage =
 
= Usage =
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* '''-f''' or '''--fastq-file''', Input fastq file (this is required)
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* '''-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)
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* '''-o''' or '''--output-file''', Output trimmed fastq file (required)
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* '''-l''' or '''--length-threshold''', Threshold to keep a read based on length after trimming. Default 20.
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* '''-x''' or '''--no-fiveprime''', Don't do five prime trimming.
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* '''-n''' or '''--trunc-n''', Truncate sequences at position of first N.
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* '''-g''' or '''--gzip-output''', Output gzipped files.
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* '''--quiet''', Don't print out any trimming information

Latest revision as of 11:15, 14 February 2017

Introduction

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.

Usage

  • -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