BWA_MEM SHORT READS

Question

[Phismil]

Dear colleagues,

I have used BWA-MEM to algin single end 50 bp reads against scaffolds. The performance is far superior compared to other aligners. However, my question is that given the recommended minimum 70 bp read length in the paper, does the recommended read length only affect the computational performance or it could "negatively" impact the robustness of the results? Many thanks in advance Arsalan

Answer 1

[ATpoint]

That is fine. Many people use this tool for that read length. If you are unsure you can also try other aligners such as bbmap, hisat2 or bowtie2 but I personally would not bother.

[Phismil]

Many thanks for your advice!