# Bowtie

Bowtie is a sequencing toolset for aligning sets of DNA into large genomes.

# Workflow

# Installing Bowtie with Spack

  • Create a spack software environment:
[flight@chead1 (mycluster1) ~]$ flight env create spack
  • Activate the environment:
[flight@chead1 (mycluster1) ~]$ flight env activate spack
  • Install bowtie:
<spack> [flight@chead1 (mycluster1) ~]$ spack install bowtie

# Running a Bowtie Job

  • Download example ecoli data:
<spack> [flight@chead1 (mycluster1) ~]$ wget -O ecoli.fq http://tiny.cc/ecoli
  • Create a job script in the current working directory:
<spack> [flight@chead1 (mycluster1) ~]$ cat << EOF > mybowtiejob.sh
#!/bin/bash -l
flight env activate spack
spack load bowtie
bowtie-build ecoli.fq e_coli
  • Submit the job to the queue:
<spack> [flight@chead1 (mycluster1) ~]$ sbatch mybowtiejob.sh

The results can then be reviewed from the slurm output file for the job in the current working directory.