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A 10x faster version base on official trimmomatic. The results of trimmomatic-pigz are exactly the same with official trimmomatic.

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shencangsheng/Trimmomatic-pigz

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Trimmomatic-pigz

A 10x faster version base on official 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

License

A short snippet describing the license (MIT)

MIT © Cangsheng Shen

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A 10x faster version base on official trimmomatic. The results of trimmomatic-pigz are exactly the same with official trimmomatic.

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