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