# 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) ~]$ flight silo file pull openflight:bowtie/ecoli.fq
  • Download an example job script to run in the current working directory:
<spack> [flight@chead1 (mycluster1) ~]$ flight silo file pull openflight:bowtie/ecoli-job.sh
  • Submit the job to the queue:
<spack> [flight@chead1 (mycluster1) ~]$ sbatch ecoli-job.sh

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