RabbitTrim version 2.0.0

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

Trimmomatic 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

Ktrim Usage

Usage: ./RabbitTrim ktrim [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
  -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
  -t,--threads INT:POSITIVE   specify the number of threads
  -p,--phred INT:{0,33,64}    specify the baseline of the phred score
  -m,--mismatch FLOAT:FLOAT in [0 - 1]
                              Set the proportion of mismatches allowed during index and sequence comparison, Default: 0.125
  -l,--minlen INT:POSITIVE    specify the minimum read size to be kept
  -q,--quality INT:POSITIVE   specify the minimum quality score
  -w,--window INT:POSITIVE    specify the window size for quality check
  -a,--seqA TEXT              specify the adapter sequence of read1
  -b,--seqB TEXT              specify the adapter sequence of read2
  -k,--seqKit TEXT:{BGI,Illumina,Nextera,Transposase}
                              specify the sequencing kit to use built-in adapters
  -c,--compressLevel INT:compression level is limited to be between 0 and 9
                              specify the compression level for the output file

Output

The output of RabbitTrim is identical to Trimmomatic and Ktrim.

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.