Bioinformatics Recipe Cookbook
Short Read Alignment

The recipe demonstrates the use of different short read aligners.

2 results • updated 19 months ago by Istvan Albert

The recipe demonstrates the use of different short read aligners.

There substantially many more differences between aligners beyond their "performance" or so-called "accuracy". Equally important is how we can customize the alignments and what additional information is produced in each of the alignments.

The recipe generates SAM alignment files with different algorithms bwa, bowtie2 in both single end and paired-end mode.

  1. Downloads the 1976 Ebola - Mayinga Reference Genome
  2. Downloads paired-end sequencing data for the 2014 outbreak
  3. Generates single-end sequence alignments with bwa and bowtie2
  4. Generates paired-end sequence alignments with bwa and bowtie2
  5. Runs samtools flagstat on each of the SAM files.

Readers are invited to investiage the SAM files to identify the differences between aligner outputs.

Lecture

A detailed presentation that explains the steps and rationale for this recipe can be found at:

Please refer to the lecture above for study materials and additional content.

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