Any alternatives to BBMap’s clumpify.sh program to optimize gzip compression?

Any alternatives to BBMap’s clumpify.sh program to optimize gzip compression?

1

I’ve had some difficulties implementing this in pipelines because it randomly fails sometimes.

Are there any other programs that can be used in its stead?


fastq


genomics


rnaseq

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because it randomly fails sometimes.

clumpify is not the program that is doing compression. BBTools programs make use of pigz library for parallel compression operations when it is available. If you do not want to use it simply add pigz=f to your commands to use system gzip program.

That said, perhaps your server is either using an older version of pigz (which you may want to get updated) or try installing it if it is not present.

There is a section of options for compression that you can play with. Check the in-line help.

If you are using multiple threads then there needs to be a sufficiently performant storage system for the read/writes to keep up. If you don’t have access to one then reducing the number of threads would be another suggestion.


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