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  • Scaffolding assembly contig with various Mate pair Library Inquiry

    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.

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