sickle - Online in the Cloud

PROGRAM:

NAME

sickle - windowed adaptive trimming tool for FASTQ files using quality

SYNOPSIS

sickle <command> [options]

DESCRIPTION

## 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 truncation 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 se -t sanger -g -f input_file.fastq -o trimmed_output_file.fastq.gz

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

`sickle pe` can operate with two types of input. First, it can take two paired-end files
as input and outputs two trimmed paired-end files as well as a "singles" file. The second
form starts with a single combined input file of reads where you have already interleaved
the reads from the sequencer. In this form, you also supply a single output file name as
well as a "singles" file. The "singles" file contains reads that passed filter in either
the forward or reverse direction, but not the other. Finally, there is an option (-M) to
only produce one interleaved output file where any reads that did not pass filter will be
output as a FastQ record with a single "N" (whose quality value is the lowest possible
based upon the quality type), thus preserving the paired nature of the data. You can also
change the length and quality thresholds for trimming, as well as disable 5'-trimming and
enable truncation 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

sickle pe -c combo.fastq -t sanger -m combo_trimmed.fastq -s
trimmed_singles_file.fastq -n

sickle pe -t sanger -g -f input_file1.fastq -r input_file2.fastq -o
trimmed_output_file1.fastq.gz -p trimmed_output_file2.fastq.gz -s
trimmed_singles_file.fastq.gz

sickle pe -c combo.fastq -t sanger -M combo_trimmed_all.fastq

Command: pe paired-end sequence trimming se single-end sequence trimming

--help, display this help and exit --version, output version information and exit

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