Workflow Steps and Code Snippets

146 tagged steps and code snippets that match keyword Trimmomatic

Command line bioinformatics workflows, created with Snakemake workflow management tool. (V0.4)

shell:
    """
    touch null.fa
    java -jar {input.exec} PE -threads {threads} -phred33 {input.forward} {input.reverse} \
    {output.forward_paired} {output.forward_unpaired} {output.reverse_paired} {output.reverse_unpaired} \
    ILLUMINACLIP:{config[trimmomatic][ILLUMINACLIP]} \
    HEADCROP:{config[trimmomatic][HEADCROP]} \
    LEADING:{config[trimmomatic][LEADING]} \
    SLIDINGWINDOW:{config[trimmomatic][SLIDINGWINDOW]} \
    TRAILING:{config[trimmomatic][TRAILING]} \
    AVGQUAL:{config[trimmomatic][AVGQUAL]} \
    MINLEN:{config[trimmomatic][MINLEN]} \
    CROP:{config[trimmomatic][CROP]}
    rm null.fa
    """

SnakeMake Trimmomatic From line 121 of master/Snakefile

High throughput Next Generation Sequencing (NGS) data analysis using Python 3 Snakemake

shell:
	"~/miniconda2/bin/trimmomatic PE -threads {threads} {input.read1} {input.read2} {output.fp} {output.fu} {output.rp} {output.ru} ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:2:keepBothReads SLIDINGWINDOW:4:20 TRAILING:3 MINLEN:36 2>{log}"

SnakeMake Trimmomatic From line 50 of master/Snakefile

Clin-mNGS: Automated pipeline for pathogen detection from clinical metagenomic data

shell:
    "trimmomatic PE {input.r1} {input.r2} {output.r1_paired} {output.r1_unpaired} {output.r2_paired} {output.r2_unpaired} SLIDINGWINDOW:5:20 MINLEN:55 LEADING:3 TRAILING:3"

SnakeMake Trimmomatic From line 51 of master/Snakefile

A Snakemake workflow to basecall, quality control and assemble Nanopore data.

shell:
    "trimmomatic PE {input.r1} {input.r2} {output.r1} {output.r1_unpaired} {output.r2} {output.r2_unpaired} -threads {params.threads} ILLUMINACLIP:{params.adapter_filepath}:{params.seed}:{params.palindrome_clip}:{params.simple_clip}:{params.minadapterlength}:{params.keep_both_reads} SLIDINGWINDOW:{params.window_size}:{params.window_size_quality} MINLEN:{params.minlength} HEADCROP:{params.headcrop_length} &>{log}"

SnakeMake Trimmomatic From line 97 of workflow/Snakefile

(S)train (A)ssignment from (M)etagen(O)me (S)NP (A)nalysis. (1.0)

shell:
    "trimmomatic PE {input.r1} {input.r2} {output.r1} {output.r1_unpaired} {output.r2} {output.r2_unpaired} -threads {params.threads} ILLUMINACLIP:{params.adapter_filepath}:{params.seed}:{params.palindrome_clip}:{params.simple_clip}:{params.minadapterlength}:{params.keep_both_reads} SLIDINGWINDOW:{params.window_size}:{params.window_size_quality} MINLEN:{params.minlength} HEADCROP:{params.headcrop_length} &>{log}"

SnakeMake Trimmomatic From line 27 of rules/trim.smk

Analysis code for the TAP-seq manuscript.

shell:
  "bash scripts/download_fastq/merge_fastq_i7.sh {params.outdir} {output.fwd} {output.rev} "
  "> {log} ; trimmomatic SE {output.rev} {params.outdir}/tmp.txt.gz CROP:58 2>> {log} ; "
  "mv -v {params.outdir}/tmp.txt.gz {output.rev} >> {log}"

SnakeMake Trimmomatic From line 103 of rules/download_fastq.smk

Benchmarking adapter and quality trimming tools

shell:
    """
    trimmomatic \
        SE \
        -phred33 \
        -threads {threads} \
        {input.fastq} \
        {output} \
        ILLUMINACLIP:gruseq.fa:2:28:10 \
        MINLEN:10 \
        2> {log}
    """

SnakeMake Trimmomatic From line 108 of master/Snakefile

An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH (v2.0)

shell: """
myoutdir="$(dirname {output.one})"
if [ ! -d "$myoutdir" ]; then mkdir -p "$myoutdir"; fi
trimmomatic PE \\
    -threads {threads} \\
    -phred33 \\
    {input.r1} {input.r2} \\
    {output.one} {output.two} \\
    {output.three} {output.four} \\
    ILLUMINACLIP:{params.adapterfile}:3:30:10 \\
    LEADING:10 \\
    TRAILING:10 \\
    SLIDINGWINDOW:4:20 \\
    MINLEN:20      
"""

SnakeMake Trimmomatic From line 74 of rules/trim_map_preprocess.smk

This workflow performs an RNA-seq analysis from the sequencing output data to the differential expression analyses. (v2.0.0)

shell:
  """
  sample=({input.sample})
  sample_trimmed=({output.sample_trimmed})
  sample_untrimmed=({output.sample_untrimmed})
  len=${{#sample[@]}}
  for (( i=0; i<$len; i=i+2 ))
  do trimmomatic PE -threads 4 ${{sample[$i]}} ${{sample[$i+1]}} ${{sample_trimmed[$i]}} ${{sample_untrimmed[$i]}} ${{sample_trimmed[$i+1]}} ${{sample_untrimmed[$i+1]}} LEADING:20 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:36
  done
  """

SnakeMake Trimmomatic From line 37 of 04_Workflow/clean.smk

Snakemake workflow: 16S rRNA-seq for gastric microbiota

shell:
    '''  
      trimmomatic PE -threads {threads} -phred33 -quiet {input.r1} {input.r2} \
      {output.r1} {output.r1_unpaired} {output.r2} {output.r2_unpaired} {params.trimmer}
    '''