I have a sets of Illumina pair-end data sets and used it as input file for de-novo genome assembler program. I have generate corresponding assembly contigs and I plan to run SSPACE for scaffolding now.

I have 4 sets of Illumina mate pair library now: PE100, Read length 100 nt, 10kb insert size, mate-pair (s_PE100_10kb_1.fastq); PE100, Read length 100 nt, 10kb insert size, mate-pair (s_PE100_10kb_2.fastq); PE100, Read length 100 nt, 5kb insert size, mate-pair (s_PE100_5kb_1.fastq); PE100, Read length 100 nt, 5kb insert size, mate-pair (s_PE100_5kb_2.fastq); PE35, Read length 35 nt, 10kb insert size, mate-pair (s_PE35_10kb_1.fastq); PE35, Read length 35 nt, 10kb insert size, mate-pair (s_PE35_10kb_2.fastq); PE35, Read length 35 nt, 5kb insert size, mate-pair (s_PE35_5kb_1.fastq); PE35, Read length 35 nt, 5kb insert size, mate-pair (s_PE35_5kb_2.fastq);

My mate pair read is range from 35 - 100 nt length and insert size is 5kb - 10kb. Can I know how I should arrange my library file for SSPACE_Standard_v3.0.pl? I not too sure how to prepare library file when my mate pair library is different read length and different insert size.

Thanks for any advice.