Algorithms

realign gaps

Coming soon

bowtie2 or other aligners use seed mapping to speed up, but also has some drawbacks in accuracy. Such as example below, bowtie2 can not deal with the gap (deletion) and the flanking sequence correctly.

• EXAMPLE 1: it does not place the gap in the correct position and reports a mismatch at the same time.

QRY: CGACG-TTTAATTAAAACAAAGCATCGCGAAGGCCCGCGGCG
     ||||. ||||||||||||||||||||||||||||||||||||
REF: CGACTGTTTAATTAAAACAAAGCATCGCGAAGGCCCGCGGCG

After realign:

QRY: CGAC-GTTTAATTAAAACAAAGCATCGCGAAGGCCCGCGGCG
     |||| |||||||||||||||||||||||||||||||||||||
REF: CGACTGTTTAATTAAAACAAAGCATCGCGAAGGCCCGCGGCG

• EXAMPLE 2: it treats the gap region near the terminal as a mutation.

QRY:    AGTGAAAAGAACTTTGAAGAGAGAGTTCAAGAGGGCGTGAAACCGTTAA
        ..|||||||||||||||||||||||||||||||||||||||||||||||
REF: (A)GTTGAAAAGAACTTTGAAGAGAGAGTTCAAGAGGGCGTGAAACCGTTAA

After realign:

QRY: AG-TGAAAAGAACTTTGAAGAGAGAGTTCAAGAGGGCGTGAAACCGTTAA
     || |||||||||||||||||||||||||||||||||||||||||||||||
REF: AGTTGAAAAGAACTTTGAAGAGAGAGTTCAAGAGGGCGTGAAACCGTTAA

Adjust gaps

Coming soon