Scythe

Scythe is a 3’ end adapter trimmer that uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. 3’ ends often include poor quality bases which need to be removed prior the quality-based trimming, mapping, assemblies, and further analysis.

The basic usage of Scythe is:

$ scythe -a adapter_file.fasta input_reads.fastq -o output_reads.fastq

The file output_reads.fastq contains the sequencing reads with removed adapters. If the adapter sequences are unknown, Scythe by itself provides Illumina adapter sequences that can be used with the -a option: illumina_adapters.fa.

More information about Scythe can found by typing:

$ scythe --help

Simple Scythe script that uses the illumina_adapters.fa file and input_reads.fastq is shown below:

#!/bin/bash
#SBATCH --job-name=Scythe
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=168:00:00
#SBATCH --mem=10gb
#SBATCH --output=Scythe.%J.out
#SBATCH --error=Scythe.%J.err

module load scythe/0.991

scythe -a ${SCYTHE_ADAPTERS}/illumina_adapters.fa input_reads.fastq -o output_reads.fastq

Scythe is single threaded program, and therefore both #SBATCH --nodes and #SBATCH --ntasks-per-node are set to 1.

The Illumina adapter sequences provided by Scythe are stored in $SCYTHE_ADAPTERS. Hence, to access the illumina adapter file use: $SCYTHE_ADAPTERS/illumina_adapters.fa.

Scythe Output

Scythe returns fastq file of reads with removed adapter sequences.

Useful Information

In order to test the Scythe (scythe/0.991) performance , we used three paired-end input fastq files, small_1.fastq and small_2.fastq, medium_1.fastq and medium_2.fastq, and large_1.fastq and large_2.fastq. Some statistics about the input files and the time and memory resources used by Scythe are shown in the table below: