BWA-MEM or BWA-ALN + BWA-SAMSE for MGI sequencing

Question

[khanhlpbao]

Hi, I just new to bioinformatics. I have some MGI single-ended NIPT sequencing, each fastq file contains multiple 50bp sequences after trimming. I have read about bwa-mem and bwa-aln + bwa-samse but I don't know what should I apply to my research. Because from what I read bwa-mem work good on > 70bp sequence and overall it has more accuracy but my sequences are just 50bp and I'm still not found any data about the effectiveness between aln and mem. Does anyone has experienced can give me advice? Thanh you very much

Answer 1

[ATpoint]

I would just use bwa-mem and stick with that. It is true that there is this 70bp recommendation but I used it before for shorter reads and it always worked fine. If you get low alignment rate you can use aln/samse and compare it, in my experience it barely makes a difference and mem is faster and easier to use.