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genomic-medicine-sweden / taxprofiler

Taxonomic profiling of shotgun metagenomic data
https://nf-co.re/taxprofiler
MIT License
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Build centrifuge database #36

Open LilyAnderssonLee opened 9 months ago

LilyAnderssonLee commented 9 months ago

Description of feature

Construct a centrifuge database including: Archaea, Bacteria, Fungi, Protozoa, Plasmid, virus, human.

LilyAnderssonLee commented 9 months ago

Memory issue caused by massive input refseq data https://github.com/DaehwanKimLab/centrifuge/issues/264.

Solution: select the represent genome for each species to decrease the input sequences size, for instance using MGnify, drep or galah