Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end. Incorrectly called bases here negatively impact assembles, mapping, and downstream bioinformatics analyses.
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. 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 drops below the threshold. At that point the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there. However, if the cut point is less than the minimum length threshold, then the read is discarded entirely.
Sickle supports four types of quality values: Illumina, Solexa, Phred, and Sanger. Note that the Solexa quality setting is an approximation (the actual conversion is a non-linear transformation). The end approximation is close.
Sickle also supports gzipped file inputs.
Sickle requires a C compiler; GCC or clang are recommended. Sickle relies on Heng Li's kseq.h, which is bundled with the source.
Sickle also requires Zlib, which can be obtained at http://www.zlib.net/.
To build Sickle, enter:
make
Then, copy or move "sickle" to a directory in your $PATH.
Sickle has two modes to work with both paired-end and single-end
reads: sickle se and sickle pe.
Running sickle by itself will give print the help:
sickle
Running sickle with either the "se" or "pe" commands will give help specific to those commands:
sickle se
sickle pe
sickle se takes an input fastq file and outputs a trimmed version of
that file. It also has options to change the length and quality
thresholds for trimming.
sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq
sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -q 33 -l 40
sickle pe takes two paired-end files as input and outputs two
trimmed paired-end files as well as a "singles" file. The "singles"
file contains reads that passed filter in one of the paired-end files
but not the other. You can also change the length and quality
thresholds for trimming.
sickle pe -f input_file1.fastq -r input_file2.fastq -t sanger \
-o trimmed_output_file1.fastq -p trimmed_output_file2.fastq \
-s trimmed_singles_file.fastq
sickle pe -f input_file1.fastq -r input_file2.fastq -t sanger \
-o trimmed_output_file1.fastq -p trimmed_output_file2.fastq \
-s trimmed_singles_file.fastq -q 12 -l 15