Paired-end read support about minia

[tseemann]

@mictadlo shuffleReads just interleaves R1 and R2. FLASH overlaps them into single end reads where possible. You should probably use FLASH before using any assembler which only supports SE reads.

[rchikhi]

Hi, indeed, as per the manual: "Giving paired or mate-pairs reads as input is OK, but keep in mind that Minia won't use pairing information. "
Pairing is used when scaffolding. You may use the following pipeline that combines Minia with the BESST scaffolder: https://github.com/GATB/gatb-minia-pipeline