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OpenGene / AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
MIT License
206 stars 51 forks source link

Pack (gzip) output good and bad reads #14

Open serge2016 opened 7 years ago

serge2016 commented 7 years ago

I think it would be great to pack the output reads (good & bad)!

sfchen commented 7 years ago

Will add an option to support gzip the output files after processing is done.

serge2016 commented 7 years ago

Moreover, maybe it would be better to use .good.fastq instead of .good.fq? It seams to me more common.

sfchen commented 7 years ago

I think fq is enough imformative for fastq, but I will consider your suggestion:)

sfchen commented 6 years ago

gzip output has been enabled on master branch.

For gzipped input, then the output will be also gzipped. If the input is not gzipped, you can enable --gzip or -z option to force gzip compression.

gzip input --> gzip output
ungzip input --> ungzip output
ungzip input + --gzip (-z) option --> gzip output

Use --compression to change the compression level (0~9), default is 2. The better the compression, the lower the speed.