Trimmomatic

We use Trimmomatic (version 0.36) to trim off residual Illumina adapters that were left behind after demultiplexing.

Here we use a set TruSeq Illumina adapters. However, if running this on your own data and you know you have different adapters, you'll want to input them in the configfile (see params section, below). If you're using the right adapters, you should see that some of the reads are trimmed; if they’re not, you won’t see anything get trimmed.

See this excellent paper on trimming parameters by MacManes 2014.

Trimmomatic Command

Based on recommendations from MacManes 2014, we use this command by default:

TrimmomaticPE ${base}.fastq.gz ${baseR2}.fastq.gz \
    ${base}.qc.fq.gz s1_se \
    ${baseR2}.qc.fq.gz s2_se \
    ILLUMINACLIP:TruSeq3-PE.fa:2:40:15 \
    LEADING:2 TRAILING:2 \
    SLIDINGWINDOW:4:15 \
    MINLEN:25

However, the trimming command can be extensively modified via the configfile. Here's how the parameters for the command above look in our config:

trimmomatic:
  trim_cmd:  "ILLUMINACLIP:{}:2:40:15 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:15 MINLEN:25"
  extra: ''

Quickstart

Run Trimmomatic via the "default" Eel Pond workflow or via the preprocess subworkflow. To run Trimmomatic as a standalone program, see "Advanced Usage" section below.

Output files:

Your main output directory will be determined by your config file: by default it is BASENAME_out (you specify BASENAME).

Trimmomatic will output files in the preprocess subdirectory of this output directory. All outputs will contain *.trim.fq.gz.

Modifying Params for Trimmomatic:

Be sure to set up your sample info and build a configfile first (see Understanding and Configuring Workflows).

To see the available parameters for the trimmomatic rule, run

elvers config trimmomatic --print_params

In here, you'll see a section for "trimmomatic" parameters that looks like this:

  ####################  trimmomatic  ####################
trimmomatic:
  adapter_file:
    pe_path: ep_utils/TruSeq3-PE-2.fa
    se_path: ep_utils/TruSeq3-SE.fa
  trim_cmd: ILLUMINACLIP:{}:2:40:15 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:35
  extra: ''
  #####################################################

Override default params by modifying these lines. In addition to changing parameters we've specifically enabled, you can modify the "extra" param to pass any extra trimmomatic parameters, e.g.:

  extra: 'HEADCROP:5' # to remove the first 5 bases at the front of the read.

See the Trimmomatic documentation for parameters and options you can pass to Trimmomatic. Be sure the modified lines go into the config file you're using to run elvers (see Understanding and Configuring Workflows).

Advanced Usage: Running Trimmomatic as a standalone rule

You can run trimmomatic as a standalone rule, instead of withing a larger elvers workflow. However, to do this, you need to make sure the input files are available.

For Trimmomatic, the input files are your input data - either downloaded or linked into the input_data directory via get_data.

If you've already done this, you can run:

elvers my_config trimmomatic

If not, you can run both at once to make sure trimmomatic can find its input files:

elvers my_config get_data trimmomatic

Snakemake Rule

We use a local copies of the trimmomatic snakemake wrappers to run Trimmomatic.

For snakemake afficionados, see the trimmomatic rules on github.