Difference between revisions of "Sickle"
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= Usage = | = Usage = | ||
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| + | * '''-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 | ||
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
