Modified the function of --metaphlan-option
in humann2 pipeline. Modifications include:
- make
--metaphlan-option
acceptmetaphlan2.bowtie2out --input_type bowtie2out
- If the output of BowTie2 from Metaphlan2 is given, the modified version of humann2 will
- ignore the option
--bowtie2db METAPHLAN_BOWTIE2_DB
(This seems to make you get 100% unclassified results. Test on MetaPhlAn version 2.7.7) - re-running MetaPhlAn by using the BowTie2 output
- copy the BowTie2 output to the Humann2 temp directory and rename it as
[filename]_metaphlan_bowtie2.txt
- ignore the option
pip install git+https://github.com/dytk2134/humann2.git
- This repository was cloned from humann2.
- For complete documentation, please see the HUMAnN2 User Manual.
Franzosa EA*, McIver LJ*, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Schwarzberg Lipson K, Knight R, Caporaso JG, Segata N, Huttenhower C. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods 15: 962-968 (2018).