# sickle - A windowed adaptive trimming tool for FASTQ files using quality

## About

Most modern sequencing technologies produce reads that have
deteriorating quality towards the 3'-end and some towards the 5'-end as well. Incorrectly called bases
in both regions 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 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.  5'-end trimming can be disabled.

Sickle also has an option to discard reads with any Ns in them.

Sickle supports three types of quality values: Illumina, Solexa, 
and Sanger. Note that the Solexa quality setting is an approximation
(the actual conversion is a non-linear transformation). The end
approximation is close. Illumina quality refers to qualities encoded
with the CASAVA pipeline between versions 1.3 and 1.7.  Illumina quality
using CASAVA >= 1.8 is Sanger encoded.

Note that Sickle will remove the 2nd fastq record header (on the "+" line) and replace it
with simply a "+". This is the default format for CASAVA >= 1.8.

Sickle also supports gzipped file inputs. There is also a sickle.xml file
included in the package that can be used to add sickle to your local [Galaxy](http://galaxy.psu.edu/) server.

## Requirements 

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/>.

## Building and Installing Sickle

To build Sickle, enter:

    make

Then, copy or move "sickle" to a directory in your $PATH.

## Usage

Sickle has two modes to work with both paired-end and single-end
reads: `sickle se` and `sickle pe`.

Running sickle by itself will 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 Single End (`sickle se`)

`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, as well as disabling 5'-trimming and enabling removal
of sequences with Ns.

#### Examples

    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 se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -x -n

### Sickle Paired End (`sickle pe`)

`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, as well as disable 5'-trimming and enable removal
of sequences with Ns.

#### Examples

    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

	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 -n