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09_GENOME_DEREPLICATION

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eolesin edited this page Jun 8, 2021 · 21 revisions

Run anvi-summarize on the dastool consensus bins

Do this to get the genomes out of anvio and into FASTA format.

#Rename the bin contigs Include the original sample name in addition to the bin info. Within the ANVI-SUMMARIZE output folder:

for i in `cat AMOR_2020_Good`; 
    do 
    bin_names=$(ls ${i}/bin_by_bin)
    for j in $bin_names; do sed -i "s/>/>${i}_/g" ${i}/bin_by_bin/${j}/${j}-contigs.fa; done
done

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