# 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 -U SAMPLE_single_reads.fastq --no-unal -p 12 -S SAMPLE.sam

  -1            read 1 of paired reads
  -2            read 2 of paired reads
  -U            single unpaired reads
  -S SAMPLE.sam write bowtie2 output in SAM format to file SAMPLE.sam
  --no-unal     ignore reads that failed to align
  -p 12         use up to 12 parallel processors

→ SAMtools to filter and convert result of SAMPLE.sam

→ Tablet-viewer to graphically view the mapped read alignment

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read more
http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

alternative short-read mapper
Burrows-Wheeler Aligner (BWA)
kallisto