I tried using MetaPhlAn-3 for profiling my shotgun metagenome sequence from Nova-seq, I have few doubts and queries for utilizing the best of MetaPhlAn-3.
- MetaPhlAn can be used for environmental samples too or is it just for human samples only?
- I tried the basic command :
metaphlan --bowtie2db ~/Documents/MetaPhlAn-3/MetaPhlAn3-DB/ ~/Documents/FLOOR-METAGENOME-NOVASEQ/CAT_FASTQ_FILES/M2_S60_R1_fastq.gz ~/Documents/FLOOR-METAGENOME-NOVASEQ/CAT_FASTQ_FILES/M2_S60_R2_fastq.gz --bowtie2out M2-S60.bowtie2.bz2 --nproc 12 --input_type fastq
It gave me profile.txt file with just the bacterial information. But when I tried to blast my sequences and get taxonomy though MEGAN6 I am getting Bacterial, Archeal, Eukaryotes as well as few viral clades too.
I used the latest database which is mpa_v30_CHOCOPhlAn_201901
- Is there any place where you have explained about the parameters which are used in metaphlan3?
- What can I do to get results for All domains(Eukaryotic, Archeal, Bacterial and viral) as you have mentioned in your introduction about metaphlan3?