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MetagenomePart3.md

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Prepping files for Anvio

  • Tom Delmont, Antti Karkman, Jenni Hultman*

Go to your co-assembly folder and make a new folder called ANVIO

mkdir ANVIO
cd ANVIO

We need to do some tricks for the contigs from assembly before we can use them on Friday. You'll need to upload biokit and activate Anvio

module load biokit
source activate anvio3

Rename the scaffolds and select those >2,500nt

anvi-script-reformat-fasta ../final.contigs.fa -l 2500 --simplify-names --prefix MEGAHIT_co_assembly -r REPORT -o MEGAHIT_co-assembly_2500nt.fa

Generate CONTIGS.db

anvi-gen-contigs-database -f MEGAHIT_co-assembly_2500nt.fa -o MEGAHIT_co-assembly_2500nt_CONTIGS.db -n MEGAHIT_co-assembly

Run HMMs to identify single copy core genes for Bacteria and Archaea, plus rRNAs

anvi-run-hmms -c MEGAHIT_co-assembly_2500nt_CONTIGS.db -T 10

Run COGs

anvi-run-ncbi-cogs -c MEGAHIT_co-assembly_2500nt_CONTIGS.db -T 10

Export GENES

anvi-get-dna-sequences-for-gene-calls -o gene-calls.fa -c MEGAHIT_co-assembly_2500nt_CONTIGS.db