Originally posted by seb567
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Technically the CASAVA pipeline will allow more mismatches (just pass a higher number with the --mistmatches parameter) but it will fail if there is a collision between barcodes caused by allowing multiple mismatches per index. For example:
TruSeq Index #18 == GTCCGC
TruSeq Index #19 == GTGAAA
Now suppose your encounter an index read which is GTCCAA. How do you resolve the conflict of this being #18 with the GC->AA at the end OR #19 with GA->CC in the middle. Unless you very carefully choose the mixture of barcodes you are likely to encounter these types of collisions when allowing more than one error per index read.
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