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.
bwa
and bowtie2
bwa
and bowtie2
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:
Please refer to the lecture above for study materials and additional content.