I want to assemble paired-end sequences and mate-pair sequences (HiSeq2000) together using SOAPdenovo.
On SOAPdenovo home page, mate-pair usage is written as follows: "Mate-pair relationship could be indicated in two ways: two sequence files with reads in the same order belonging to a pair, or two adjacent reads in a single file (FASTA only) belonging to a pair." (http://soap.genomics.org.cn/)
How can I convert raw mate-pair FASTQ file into proper format for SOAPdenovo assembly? Is there any converting script?