Question

any fast PRINSEQ alternative?

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6.1 years ago

garbanyo • 0

Hi all, I'm writing a C++ version of PRINSEQ to filter and trim fastq files and I want to do some timing/memory usage comparison with other sequencing QC tools. Is there any tool beside FastQC, Fastx toolkit and the perl version of PRISEQ that I should include?

Thanks a lot

sequence sequencing next-gen • 1.7k views

ADD COMMENT • link updated 4.5 years ago by milad eidi ▴ 20 • written 6.1 years ago by garbanyo • 0

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123Fastq, can do all NGS reads pre-processes fast in a highly interactive graphical user interface.

ADD REPLY • link 4.5 years ago by milad eidi ▴ 20

score 1 · Answer 1 · 2018-03-21

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6.1 years ago

WouterDeCoster 47k

Have a look at fastp

ADD COMMENT • link 6.1 years ago by WouterDeCoster 47k

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will do, thanks a lot

ADD REPLY • link 6.1 years ago by garbanyo • 0

score 1 · Answer 2 · 2018-03-21

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6.1 years ago

GenoMax 141k

bbduk.sh from BBMap suite. Java but multi-threaded and plenty fast for me.

ADD COMMENT • link 6.1 years ago by GenoMax 141k