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First, divide up your samples into about 1 million reads per file, forward and reverse reads separately.
perl ~/bin/split_fastq_qiime_1.8.pl|../../../../../../../../../download/attachments/91590224/ split_fastq_qiime_1.8.pl ?version=2&modificationDate=1394040210338\ <read> <number needed> <output prefix>
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Then, overlap each of the 100 files with SHERA where ${PBS_ARRAYID} is the process number for parallel processing:
perl concatReads_1.8.pl|../../../../../../../../../download/attachments/91590224/ concatReads_1.8.pl ?version=1&modificationDate=1394040328360\ fastq_1 fastq2 --qualityScaling illumina
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perl fix_index.pl 131001Alm_D13-4961_1_sequence.split.${PBS_ARRAYID}.filter_0.8.fastq 131001Alm_D13-4961_3_sequence.fastq > 131001Alm_D13-4961_3_${PBS_ARRAY_ID}.filter_0.8.fastqOrfastq
Or, if you have to generate it from the header (if the index is already present in the header):
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