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Create bowtie2 index

How to create a bowtie2 index database of multiple genomes?

Example of creating a bowtie2-index based on E. coli reference genomes.

# Merge all E. coli reference genomes into one genomes.fna file
cat ref_genomes/ecoli/*.fna > genomes.fna

# create bowtie2 index database (database name: ecoli)
bowtie2-build genomes.fna ecoli

# result: 6 .bt2 database files
ls
ecoli.1.bt2
ecoli.2.bt2
ecoli.3.bt2
ecoli.4.bt2
ecoli.rev.1.bt2
ecoli.rev.2.bt2

# use 'inspect' to check the content of your database
bowtie2-inspect -n ecoli

# define your BOWTIE2_INDEXES directory and move the database files into it
export BOWTIE2_INDEXES=/path/to/my/bowtie2/databases/
cp *.bt2 $BOWTIE2_INDEXES



# in bowtie2 mapping, database is defined by option -x
bowtie2 -x ecoli ...