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FANSe2: A Robust and Cost-Efficient Alignment Tool for Quantitative Next-Generation Sequencing Applications

Figure 2

Rational and validation of the iterative strategy of FANSe2.

(A) Errors in a read which can be perfectly detected by FANSe algorithm versus the seed length for 50-, 75- and 100-nt reads, respectively. (B) Theoretical miss rate of FANSe algorithm with different seed length for various read length. (C) Error distribution of six sequencing datasets (listed in Table S1 in File S1) sequenced on various types of sequencers, respectively. Reads were mapped with FANSe. ARL = average read length. (D, E) Mapping the E. coli mRNA dataset reported in [5]. For FANSe2 algorithm, the reads mapped (D) and the calculation time (E) used using different read length stages were shown in colors. The test was performed in a quad-core Intel i5-3570K computer using one CPU core.

Figure 2