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安装环境

Ubuntu18.10
Trimmomatic Version 0.38: binary

安装过程

在此网站http://www.usadellab.org/cms/index.php?page=trimmomatic下载Trimmomatic的binary解压后得到trimmomatic-0.38.jar
各种操作都是用java调用这个jar包

试用Trimmomatic

Paired End:

java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

This will perform the following:

Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10)
Remove leading low quality or N bases (below quality 3) (LEADING:3)
Remove trailing low quality or N bases (below quality 3) (TRAILING:3)
Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15)
Drop reads below the 36 bases long (MINLEN:36)

Single End:

java -jar trimmomatic-0.35.jar SE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

This will perform the same steps, using the single-ended adapter file

使用下面语句试了single end
···
java -jar trimmomatic-0.38.jar SE simulatedReads.fastq result.fq.gz ILLUMINACLIP:adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
TrimmomaticSE: Started with arguments:
simulatedReads.fastq result.fq.gz ILLUMINACLIP:adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Automatically using 4 threads
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Quality encoding detected as phred33
Input Reads: 1050000 Surviving: 1050000 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully
···

介绍

Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem depending on the library preparation and downstream application.
There are two major modes of the program: Paired end mode and Single end mode. The paired end mode will maintain correspondence of read pairs and also use the additional information contained in paired reads to better find adapter or PCR primer fragments introduced by the library preparation process.
Trimmomatic works with FASTQ files (using phred + 33 or phred + 64 quality scores,
depending on the Illumina pipeline used). Files compressed using either „gzip‟ or „bzip2‟ are supported, and are identified by use of „.gz‟ or „.bz2‟ file extensions.