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mozack / abra

Assembly Based ReAligner
MIT License
70 stars 12 forks source link

Testing practices #40

Closed ionox0 closed 6 years ago

ionox0 commented 6 years ago

Thank you for your work on this project,

I was wondering if you had any suggestions for testing Abra in a pipeline. For example, with a very small pair of fastqs, say only a few reads, are there any parameters or suggestions that would make an Abra run only take a few seconds? Thank you

mozack commented 6 years ago

The biggest issue in this case will be loading the reference. If you can use a small reference, small input bam and a single target region specified in the bed file, the runtime should be in the seconds range.

ionox0 commented 6 years ago

Great, thanks for the suggestion, yes I think with that change it will be very quick