TRIMMOMATICPE(1)

✨ NAME ✨

Welcome to the Trimmomatic Manual, bestie 🎀 Here's the lowdown on TrimmomaticPE, a flexible read trimming tool for Illumina NGS data 💅

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🦋 SYNOPSIS 🦋

Paired End Mode:

TrimmomaticPE [-threads threads] [-phred33 | -phred64] [-trimlog logFile] paired output 1 unpaired output 1 paired output 2 unpaired output 2 step 1 ...

Single End Mode:

TrimmomaticSE [-threads threads] [-phred33 | -phred64] [-trimlog logFile] output step 1 ...

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🌸 DESCRIPTION 🌸

Okay so, Trimmomatic is literally a whole vibe for trimming illumina paired-end and single ended data 🧚 It can do a variety of useful trimming tasks, and you choose which steps to run and how they're set up right on the command line. No cap, it's so customizable 💖

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👑 OPTIONS 👑

• -phred — No quality score specified? No stress, phred-64 is the default 🙈
• -trimlog — Pass in a trimlog file and Trimmomatic keeps a log of every read trimming, with these details 📝
  • the read name
  • the surviving sequence length
  • the location of the first surviving base, aka. the amount trimmed from the start
  • the location of the last surviving base in the original read
  • the amount trimmed from the end

Multiple steps can be stacked by adding more arguments at the end, as many as you need 🌈

Most steps take one or more settings, separated by : (a colon) 💅

Step options 🍓

• ILLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>
  • fastaWithAdaptersEtc: the path to a fasta file holding all the adapters, PCR sequences etc. How each sequence is named inside that file decides how it gets used, so see below 👀
  • seedMismatches: the maximum mismatch count that still allows a full match to be performed 🎯
  • palindromeClipThreshold: how accurate the match between the two "adapter ligated" reads has to be for PE palindrome read alignment 🔍
  • simpleClipThreshold: how accurate the match between any adapter etc. sequence has to be against a read 🧐
  • The adapters are installed on the Debian system at /usr/share/trimmomatic/ 🐧
• SLIDINGWINDOW:<windowSize>:<requiredQuality>
  • windowSize: the number of bases to average across 🪟
  • requiredQuality: the average quality you require 💯
• LEADING:<quality>
  • quality: the minimum quality required to keep a base ✨
• TRAILING:<quality>
  • quality: the minimum quality required to keep a base ✨
• CROP:<length>
  • length: the number of bases to keep, counting from the start of the read ✂️
• HEADCROP:<length>
  • length: the number of bases to remove from the start of the read 🫧
• MINLENGTH:<length>
  • length: the minimum length of reads to be kept 🦋

Trimming Order 🎀

Trimming happens in the order the steps are specified on the command line. It's recommended in most cases that adapter clipping, if you need it, happens as early as possible ⭐

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🧚 EXAMPLES 🧚

Paired End:

TrimmomaticPE s_1_1_sequence.txt.gz s_1_2_sequence.txt.gz lane1_forward_paired.fq.gz lane1_forward_unpaired.fq.gz lane1_reverse_paired.fq.gz lane1_reverse_unpaired.fq.gz ILLUMINACLIP:/usr/share/trimmomatic/illuminaClipping.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

This is what it's giving 🔥

• Remove adapters
• Remove leading low quality or N bases (below quality 3)
• Remove trailing low quality or N bases (below quality 3)
• Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15
• Drop reads that come out below 36 bases long

The equivalent for single-ended reads is giving the same main character energy 💜

TrimmomaticSE s_1_1_sequence.txt.gz lane1_forward.fq.gz ILLUMINACLIP:/usr/share/trimmomatic/illuminaClipping.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

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That's the whole tea, bestie 🫶 You just read TRIMMOMATICPE(1) from Trimmomatic 0.22, dated July 2012 👑💖