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Repository sickle
Name: sickle
Owner: iuc
Synopsis: A windowed adaptive trimming tool for FASTQ files using quality
Sickle is a tool that uses sliding windows along with quality and length
thresholds to determine when quality is sufficiently low to trim the 3'-end
of reads and also determines when the quality is sufficiently high enough to
trim the 5'-end of reads. It will also discard reads based upon the length
threshold. It takes the quality values and slides a window across them whose
length is 0.1 times the length of the read. If this length is less than 1,
then the window is set to be equal to the length of the read. Otherwise, the
window slides along the quality values until the average quality in the window
rises above the threshold, at which point the algorithm determines where
within the window the rise occurs and cuts the read and quality there for the
5'-end cut. Then when the average quality in the window drops below the
threshold, the algorithm determines where in the window the drop occurs and
cuts both the read and quality strings there for the 3'-end cut. However, if
the length of the remaining sequence is less than the minimum length
threshold, then the read is discarded entirely (or replaced with an "N"
record). 5'-end trimming can be disabled.
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/sickle
Type: unrestricted
Revision: 6:6756c87dc2d4
This revision can be installed: True
Times cloned / installed: 930

Contents of this repository

Name Description Version Minimum Galaxy Version
windowed adaptive trimming of FASTQ data 1.33.2 17.01

Categories
Fastq Manipulation - Tools for manipulating fastq data
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis