Fig. 2
Examples for adapter trimming. Pictures show the relative position of an adapter and a read, and the expected result after processing with the adapter_filter function of FastqCleaner. Dotted lines indicate the portion of the read that will be removed. Arrows show the direction along the read used for the program to seek for matches. If one or more matches are found, the function trims the longest subsequence, that contains the matching region plus the rest of the read, in the corresponding trimming direction. a partial adapter on the right + right-trimming of anchored adapter. b partial adapter on the left + left-trimming of anchored adapter. c partial adapter within read + right-trimming. D,E: full match between an adapter and a portion of the read + left- (d) or right- (e) trimming. f multiple matches for a same adapter + left-trimming