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.
Downloads the 1976 Ebola - Mayinga Reference Genome
Downloads paired-end sequencing data for the 2014 outbreak
Generates single-end sequence alignments with bwa and bowtie2
Generates paired-end sequence alignments with bwa and bowtie2
Runs samtools flagstat on each of the SAM files.
Readers are invited to investiage the SAM files to identify the differences between aligner outputs.
A detailed presentation that explains the steps and rationale for this recipe can be found at: