which database to use - Githubissues

bioinformatics-centre / kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

http://kaiju.binf.ku.dk

GNU General Public License v3.0

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which database to use #67

Closed chloelulu closed 6 years ago

chloelulu commented 6 years ago

Hi, I saw there are five database in Kaiju http://kaiju.binf.ku.dk/server I plan to use Kaijun to analysis the shotgun metagenomics data with 100bp pair-ended reads(Hiseq). I am wondering which to use. I just want to classify bacteria and archaea. Confusing. I have used kraken, only 3% of the reads can got hits. So I want to try Kaiju, since as it published in the paper, which showed much more hits of reads for environmental samples. Thanks in advanced.

pmenzel commented 6 years ago

Hi, if you are just interested in bacteria and Archaea, then just use the "NCBI BLAST nr" database.