Background: With the advent of the second generation sequencing technology, the discovery of sequence
alignment and sequence variation is a long-standing challenge.
Results: A method based on general alignment software, SNP and Indel software tools was proposed in this paper. By
comparing the advantages of traditional alignment software, we can produce the best alignment. SNP and Indel detection
tools fusion research found that different depth of sequencing effect is different. When the sequence depth reaches a certain
value, select one of the software for testing.
Conclusions: Finally, the experimental verification shows that SNP and Indel have certain advantages in the comparison of
the effects of the fusion method.