biocore / oecophylla

shotgun pipeline
MIT License
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updated Centrifuge and others #124

Closed qiyunzhu closed 7 years ago

qiyunzhu commented 7 years ago

Based on the feedbacks from the Centrifuge development team, I removed Bracken post-processing of Centrifuge result, but just used the Kraken-style report directly produced by Centrifuge as the final result. This report files contains read counts and relative abundances per taxon.

Therefore I also added the combine_kraken function. This function handles the Kraken-style reports. In oecophylla, it actually processed Centrifuge output instead of Kraken output.

Meanwhile, the old combine_centrifuge function is retained, because it directly handles the native Centrifuge output file (not Kraken-style report). This native output file contains read counts and relative abundances per genome, which is not what we want.

Also tested the recently release Kraken 1.0.

Addressed issues #121 and #122

qiyunzhu commented 7 years ago

@tanaes @sjanssen2 @mortonjt