How to run the BOWTIE short read aligner

How to run the BOWTIE short read aligner

This recipe demonstrates the use of the BOWTIE short read aligner to create a BAM file.

1 result • updated 25 days ago by Istvan Albert

This recipe demonstrates the use of the BOWTIE short read aligner to create a BAM file.

Steps demonstrated in the recipe:

  1. Connecting to NCBI to download the Ebola reference genome.
  2. Connecting to the Short Read Archive to download high throughput sequencing data
  3. Indexing the Ebola reference genome with bowtie2-build
  4. Aligning the short reads to the Ebola genome with bowtie2 to produce a SAM file.
  5. Converting and sorting the SAM file into the BAM format.
  6. Generating statistics report on the resulting BAM file.

For more information see:

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