`RabbitTrim version 1.0.0`

RabbitTrim is an efficient adapter removal tool based on Trimmomatic, which implemented in C++ and deeply optimized in performance. RabbitTrim refactors and improves the efficiency of Trimmomatic in processing plain FASTQ data and gzip-compressed data. RabbitTrim supports all function modules available in Trimmomatic and maintains identical results.

Installation

RabbitTrim is written in C++ for GNU Linux/Unix platforms.

Dependancy

cmake version 3.20 or later [REQUIRED]
gcc version 9.4.0 or later [REQUIRED]
zlib [REQUIRED]
intel isa-l [OPTIONAL]

Compile and install

git clone https://github.com/RabbitBio/RabbitTrim.git
cd RabbitTrim
mkdir build && cd build
cmake .. -DIGZIP_PATH=[your installation path for intel isa-l]
make -j

Usage

Usage: ./RabbitTrim trimmomatic [OPTIONS]

Options:
  -h,--help                   Print this help message and exit
  -P,--PE,--no-PE{false} Needs: --forward --reverse Excludes: --SE
                              specify whether to be pair end data
  -S,--SE,--no-SE{false} Needs: --forward Excludes: --PE --reverse
                              specify whether to be single end data
  -t,--threads INT:POSITIVE   specify the number of threads
  -p,--phred INT:{0,33,64}    specify the baseline of the phred score
  -f,--forward TEXT:PATH(existing) ...
                              specify the path to the forward read file
  -r,--reverse TEXT:PATH(existing) ... Excludes: --SE
                              specify the path to the reverse read file
  -o,--output TEXT REQUIRED   specify the path to the output file
  --log TEXT                  specify the path to the trim log file
  --stats TEXT REQUIRED       specify the path to the trim statistical data file
  -s,--steps TEXT ... REQUIRED
                              specify the steps to be performed
  -c,--compressLevel INT:compression level is limited to be between 0 and 9
                              specify the compression level for the output file
  --quiet,--no-quiet{false}   specify whether to print program runtime information
  --validatePair,--no-validatePair{false}
                              specify whether to validate pair data
                              specify the max thread number of pigz

Example

Process plain FASTQ data in simple mode (for Single-End data)

./RabbitTrim trimmomatic --SE -f /data/demo.read1.fastq -o /data/output/out.fastq --stats /data/output/trim_stat -s ILLUMINACLIP:../adapter/TruSeq-DNA-Free-SE.fa:2:30:12:1:true MINLEN:36 -p 33 -t 1

Process plain FASTQ data in palindrome mode (for Paired-End data)

./RabbitTrim trimmomatic --PE -f /data/demo.read1.fastq -r /data/demo.read2.fastq -o /data/output/out.fastq --stats /data/output/trim_stat -s ILLUMINACLIP:../adapter/TruSeq-DNA-Free-PE.fa:2:30:12:1:true MINLEN:36 -p 33 -t 1

Process gzip-compressed data in simple mode (for Single-End data)

./RabbitTrim trimmomatic --SE -f /data/demo.read1.fastq.gz -o /data/output/out.fastq.gz --stats /data/output/trim_stat -s ILLUMINACLIP:../adapter/TruSeq-DNA-Free-SE.fa:2:30:12:1:true MINLEN:36 -p 33 -t 1

Process gzip-compressed data in palindrome mode (for Paired-End data)

./RabbitTrim trimmomatic --PE -f /data/demo.read1.fastq.gz -r /data/demo.read2.fastq.gz -o /data/output/out.fastq.gz --stats /data/output/trim_stat -s ILLUMINACLIP:../adapter/TruSeq-DNA-Free-PE.fa:2:30:12:1:true MINLEN:36 -p 33 -t 1

Output

The output of RabbitTrim is identical to Trimmomatic. For single-end data, it typically includes one processed FASTQ file (either plain or gzip-compressed format) and one trimming information statistics file. For paired-end data, it typically includes four FASTQ files and one trimming information statistics file.

Bug Report

We highly appreciate all bug reports, comments, and suggestions from our users.
Please feel free to raise any concerns or feedback with us without hesitation by issue.

RabbitBio/RabbitTrim

RabbitTrim version 1.0.0