BWA-MEM Vs BWA-ALN

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8.5 years ago

SOHAIL ▴ 410

Hi everyone,

I'm sorry if it is answered anywhere else, I have raw dna-seq paired-end sequence reads data from different libraries of read length for different samples. Ranging from 50-90, 50-101, 50-150 (after quality trimming). In FASTQC check i noticed that about 10% of reads are lesser than 70 bp for each sample.

As BWA-mem is pretty mature now but the bwa docs say that bwa mem is preferable for longer reads ( > 70 bp). and BWA-aln is good for shorter reads, but i guess most of the reads from my library are not shorter.

I want to use one mapping algorithm for consistency reasons.Can i still use bwa-mem ignoring small fraction of smaller read lengths? or i should use BWA-aln ?

Thanks

sohail

next-gen genome alignment • 11k views

ADD COMMENT • link 8.5 years ago by SOHAIL ▴ 410

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bwa-mem could be used for short reads as well, but this blog suggests that bwa-aln performs better for 50bp reads but over all mem has a good accuracy at different mismatch levels. Would it be useful if you align the 10% of the short reads with mem and aln and compare the stats to see if it makes a big difference.