For paired-end sequences, after trimming, the two ends are not "synchronized": some pairs will get one end passed while the other end failed. A simple and not-optimized script is provide to re-synchronize the reads. The perl program is in the same site as paired_end_trim.pl. To use it, btrim should be used using the "-s" option to write a summary file for each end. For example: trim -a 25 -q -t s_8_1_sequence.txt -o s_8_1.25 -s s_8_1.sum25 trim -a 25 -q -t s_8_2_sequence.txt -o s_8_2.25 -s s_8_2.sum25 paired_end_trim.pl s_8_1.sum25 s_8_2.sum25 s_8_1.25 s_8_2.25 Four files will be created: two files (*.pe) are for reads that both ends passed trimming. The reads are in the same order so they can be used as pe reads. Another two files (*.se) are for those reads that only one end passed trimming. They can be used as se reads. Yong Kong Yale University