How toÂ

Run flash on the two fastq's, a la:
```
flash Ustilago-5_S9_L001_R1_001.fastq Ustilago-5_S9_L001_R2_001.fastq
```
This generates "out.extendedFrags.fastq" of the stitched reads.
Then run revcomp_fastq on the result - this script will correct the orientation of reads and trim the 454 emPCR primer sequences, giving you two files ready for qiime as described here.
```
./revcomp_fastq out.extendedFrags.fastq > seqs.fq 2> bc.fq
```

Space shortcuts