General reads set trimmer

Description

This tool is a general trimming tool for FASTQ or FASTA formatted reads files. It contains all the trimming methods used in the PRINSEQ package, including the poly-A/T and quality methods that are available as separate trimming tools too.

Details

When you launch the trimming tool, only those trimming methods, for which some value is assigned, are used. You can use several trimming methods in the same time. Form example trimming with parameters Trim left: 3 and Trim right: 10 would produce a reads set where all the reads are trimmed by removing 3 bases form the 5'-end and 10 bases from the 3'-end.

For detailed descriptions of the different trimming conditions, please check the manual of the PRINSEQ package. From the table below, you can check what PRINSEQ command line options the parameter definitions correspond:
Parameter namecommand line optionDescription
Trim to length-trim_to_lenTrim all reads from the 3-prime-end to result in reads with this length.
Trim left-trim_leftTrim reads at the 5-prime-end by given number of positions.
Trim right-trim.rightTrim reads at the 3-prime-end by given number of positions.
Trim left tails-trim_tail_leftTrim poly-A/T tail with a minimum length of the given value at the 5-prime-end.
Trim right tails-trim_tail_rightTrim poly-A/T tail with a minimum length of the given value at the 3-prime-end.
Trim left poly-N tails-trim_ns_leftTrim poly-N tail with a minimum length of the given value at the 5-prime-end.
Trim right poly-N tails-trim_ns_rightTrim poly-N tail with a minimum length of the given value at the 3-prime-end.
Trim 5-prime-end by quality-trim_qual_leftTrim reads by quality score from the 5-prime-end with the given threshold score.
Trim 3-prime-end by quality-trim_qual_rightTrim reads by quality score from the 3-prime-end with the given threshold score.
The quality score calculation method-trim_qual_typeType of quality score calculation to use
Quality score comparison condition-trim_qual_rule Rule to use to compare quality score threshold to calculated value.
Window size for quality calculation-trim_qual_windowThe sliding window size used to calculate quality score by type. To stop at the first base that fails the rule defined, use a window size of 1.
Step size used to move the quality window-trim_qual_step TYPE INTEGER DEFAULT 1 (Step size used to move the sliding window. To move the window over all quality scores without missing any, the step size should be less or equal to the window size.
Quality data is in Phred+64 format-phred64 You should select "yes" option if the quality data in FASTQ file is in Phred+64 format. For Illumina 1.8+, Sanger, Roche/454, Ion Torrent, PacBio data, you should use the default value: no

Output

The trimmed reads are saved to file called trimmed.fastq or trimmed.fasta. You can also print out a log file that contains information about the filtering task and statistics about how many reads were accepted and rejected.

Reference

This tool is based on the PRINSEQ package.