04_MAPPING

Step 0. Prep the data for mapping to be followed by binning

Yet another loop. Round and round we go... Within the 03_ASSEMBLIES directory:

# Reformat names

for SET in `cat set.txt`
do
    anvi-script-reformat-fasta $SET/$SET-contigs.fa -l 2500 --simplify-names -o $SET.fa
    anvi-gen-contigs-database -f 04_CONTIGS/$SET.fa -o 04_CONTIGS/$SET-CONTIGS.db
done

# HMM profiling
for SET in `cat set.txt`; do anvi-run-hmms --num-threads 20 -c 04_CONTIGS/$SET-CONTIGS.db ; done

# Run against NCBI COG database
for file in ./*.db; do anvi-run-ncbi-cogs --num-threads 16 -c $file ; done

# Build bowtie2 DB for each co-assembly
for SET in `cat set.txt`
do
    bowtie2-build 03_CONTIGS/$SET.fa 04_MAPPING/$SET
done