Trimmomatic - gws_omix

Typing name : TASK.gws_omix.Trimmomatic

Brick : gws_omix

Eliminate adapters and low-quality reads

Trimmomatic is a software tool that trims and filters high-throughput sequencing data. It removes adapter sequences, low-quality reads, and other unwanted artifacts. Compatible with both single-end and paired-end data.

Outputs are named so that, for paired-end data, the final files become: trimmed{Forward_separator}.fastq.gz trimmed{Reverse_separator}.fastq.gz Then HISAT2 or any other aligner can detect them using the same Forward/Reverse separators.

Input

FASTQ Folder

Folder containing raw FASTQ reads

Fastq folder

Output

Trimmed Reads

Folder containing trimmed FASTQ files

Fastq folder

Configuration

threads

Optional

Number of threads

Type : int

Default value : 2

min_len

Optional

Minimum read length to keep

Type : int

Default value : 35

sequencing_type

Choose Single-end or Paired-end

Type : string

Allowed values : Paired-end Single-end

Forward_separator

Forward read identifier (for Paired-end)

Type : string

Allowed values : R1 1 r1

Reverse_separator

Reverse read identifier (for Paired-end)

Type : string

Allowed values : R2 2 r2

5_prime_hard_trimming_read_size

Optional

Bases to remove from 5' end

Type : int