STEP 2. Full-length sequences correction

Input: Fastq file and the meta information of reads (output from STEP 1)

Output: Refined eccDNA and sequence of Full eccDNA

1. Divide reads with the same eccDNA breakpoints (with a 50 bp offset allowed) into one block Bi (i ≥ 1).

2. For each block Bi, (LSj, LEj) represents the eccDNA breakpoint coordinates of supporting read j (1 ≤ j ≤ Ji), where Ji represents the total number of reads in Bi.

a. Calculate the refined coordinates (LSi, LEi) = (Mode (LSj), Mode (LEj)).

b. Record the supporting read number Ji of (LSi, LEi).