Sickle

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