This recipe demonstrates the use of the BWA short read aligner to create a BAM file.
Steps demonstrated in the recipe:
- Connecting to NCBI to download the Ebola reference genome.
- Connecting to the Short Read Archive to download high throughput sequencing data
- Indexing the Ebola reference genome with
- Aligning the short reads to the Ebola genome with
bwa mem to produce a SAM file.
- Converting and sorting the SAM file into the BAM format.
- Generating statistics report on the resulting BAM file.
For more information see: