https://github.com/shencangsheng/trimmomatic-pigz

A 10x faster version base on official trimmomatic. The results of trimmomatic-pigz are exactly the same with official trimmomatic.
https://github.com/shencangsheng/trimmomatic-pigz

faster parallel speedup trimmomatic

Last synced: 13 days ago
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A 10x faster version base on official trimmomatic. The results of trimmomatic-pigz are exactly the same with official trimmomatic.

• Host: GitHub
• URL: https://github.com/shencangsheng/trimmomatic-pigz
• Owner: shencangsheng
• License: other
• Created: 2020-09-03T03:14:11.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2024-11-20T04:04:46.000Z (6 months ago)
• Last Synced: 2025-03-31T14:13:48.796Z (about 2 months ago)
• Topics: faster, parallel, speedup, trimmomatic
• Language: Java
• Homepage:
• Size: 131 KB
• Stars: 16
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Trimmomatic-pigz

A 10x faster version base on [official trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic). The results of trimmomatic-pigz are exactly the same with official trimmomatic.(md5sum with decompression fastq)

Download: https://github.com/jaydenSen/Trimmomatic-pigz/releases/download/v1.0/trimmomatic-pigz.jar

## Principle

We replaced gzip library with a parallelized version: pigz.

https://github.com/shevek/parallelgzip

> This library contains a parallelized GZIP implementation which is a high performance drop-in replacement for the standard java.util.zip classes. It is a pure Java equivalent of the pigz parallel compresssor.

## Benchmark test

Test in paired end Mode with two fastq.gz(R1/R2):

![image](https://github.com/jaydenSen/Trimmomatic-pigz/raw/master/benchmark-test.png)