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Table 1 Algorithm of four aligners: SOAP2, Bowtie, BWA, and Novoalign

From: How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?

 

SOAP2

Bowtie

BWA

Novoalign

(2.20)*

(0.12.3)

(0.5.8 C)

(2.07.00)

Indexing

FM-index

FM-index

FM-index

Hash table

Inexact match

Split read

Quality-aware backtracking

Backtracking

Alignment scoring

  1. *version of the program.
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BioData Mining

ISSN: 1756-0381