Tool:fastp 0.23.0 released, runs 2x faster, and generates reproducible outputs.
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11 months ago
chen ★ 2.4k

fastp, the widely used ultra-fast FASTQ preprocessing and QC tool, and till now has been cited over 2,000 times.

Today, a new version, v0.23.0 has been released, with great improvement on performance.

The threading and I/O modules have been completely rewritten to generate reproducible outputs and improve performance greatly. New libraries libisal and libdeflate were introduced to replace the slow zlib. Although this may bring some difficulties to compilation, it is all worthwhile for performance improvement.

In many cases, fastp v0.23.0 can be 2x as faster as previous versions. Especially, when the compression level is set to 6 or higher, the performance gain is very obvious.

Threading randomness issue has been addressed, so the output files are MD5 consistent when you run it twice, which means the results are completely reproducible.

Go to the new release: https://github.com/OpenGene/fastp/releases/tag/v0.23.0

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