Template:Join paired-end FASTQ

Join paired-end FASTQ

To join pared-end reads from Illumina external program fastq-join is used. Define paths to forward and reverse files obtained from Illumina run you want join, then you can select percentage of maximal difference and minimal overlap of the reads. The reads with the identical titles up to specified character (space is default) will be tested:

from Lib1_S3_L001_R1_001.fastq	from Lib1_S3_L001_R2_001.fastq
M00816:79:000000000-AADTK:1:2115:18256:2080 1:N:0:3	M00816:79:000000000-AADTK:1:2115:18256:2080 2:N:0:3

You can store joined and unpaired sequences in desired folder by "Join only FASTQ files (save as...)" button or you can load joined sequences to SEED by "Join and load FASTQ files" button.