Sickle
Sickle is a windowed adaptive trimming tool for FASTQ files using quality.
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | sickle/1.33 |
| BGSC | N/A |
Note: You can simply use module load sickle to activate the most recently installed version of this software.
Arguments / Options
This is a list of arguments for the sickle command that we wanted to highlight. Use this online man page for a full list.
Sickle has two operating modes: 'pe' (paired-end sequence trimming) and 'se' (single-end sequence trimming). The mode is set by putting either 'se' or 'pe' after the sickle command (e.g. sickle se --fastq-file myfile.fastq -o myoutput -t illumina)
| Option | Description |
|---|---|
| --fastq-file | Set the input file when in 'se' mode |
| -o | Set the output file in 'se' mode |
| -f | Input a paired-end foward fastq file in 'pe' mode |
| -r | Input a paired-end reverse fastq file in 'pe' mode |
| -o | Output a trimmed forward fastq file in 'pe' mode |
| -p | Output a trimmed reverse fastq file in 'pe' mode |
| -c | Input a combined/interleaved paired-end fastq file |
| -m | Output a combined/interleaved paired-end fastq file. Must use -s flag |
| -s | Output trimmed singles fastq file |
| -t | Quality type: solexa, illumina, sanger |
Sample Slurm Script
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load sickle/1.33 # Load sickle
sickle se -t illumina -f input.fastq -o output.fastq
Real Example
Has your research group used Sickle in a project? Contact the HPC Team and we'd be glad to feature your work.
Citation
Please include the following citation in your papers to support continued development of Sickle.
Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software]. Available at https://github.com/najoshi/sickle.