Galaxy | Tool Preview

FASTQ Trimmer (version 1.1.5)
Use Absolute for fixed length reads (Illumina, SOLiD)
Use Percentage for variable length reads (Roche/454)
Values start at 0, increasing from the left
Values start at 0, increasing from the right; use a negative value to remove everything to the right of the absolute value of the position

What is does

This tool allows you to trim the ends of reads.

You can specify either absolute or percent-based offsets. Offsets are calculated, starting at 0, from the respective end to be trimmed. When using the percent-based method, offsets are rounded to the nearest integer.

For example, if you have a read of length 36:

@Some FASTQ Sanger Read
CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA
+
=@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@

And you set absolute offsets of 2 and 9:

@Some FASTQ Sanger Read
ATATGTNCTCACTGATAAGTGGATA
+
@.@;B-%?8>CBA@>7@7BBCA4-4

Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36):

@Some FASTQ Sanger Read
ATATGTNCTCACTGATAAGTGGATATN
+
@.@;B-%?8>CBA@>7@7BBCA4-48%

Trimming a color space read will cause any adapter base to be lost.