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shuffleSequences_fastq.pl R1.fastq R2.fastq > R1_R2.fastq &
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2. Make hash of the reads using Velveth. Hash length (or kmer length) matters. You might have to run velvet several times to pick the best kmer length. It should be long enough to avoid false positives, but not long that you miss out reads in your assembly. Recommendation: try k-mer lengths between 61-73.
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