→ Install Bowtie2

Bowtie2 example

mapping short reads against E. coli 2011 outbreak genome

# Create bowtie2 index database

# example genome: German 2011 E.coli outbreak (database name: ecoli)

bowtie2-build GCF_000299455.fna ecoli

# Bowtie2 mapping

# map reads (sample.fastq) against the E. coli genome database 'ecoli'

bowtie2 -x ecoli -1 SAMPLE_R1.fastq -2 SAMPLE_R2.fastq --no-unal -p 12 -S SAMPLE.sam

-1 read 1 of paired reads

-2 read 2 of paired reads

--no-unal ignore reads that failed to align

-p 12 use up to 12 parallel processors

-S SAMPLE.sam write bowtie2 output in SAM format to file SAMPLE.sam

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SAMtools to filter and convert the bowtie2 mapping result of SAMPLE.sam

Tablet-viewer to graphically view the mapped read alignments

alternative short-read mapper

Burrows-Wheeler Aligner (BWA)