Question: I sequenced my dual indexed library as 8bp single index. Will reading only the first 8bp of the 10bp index read be sufficient for demultiplexing?
Answer: Yes, you can de-multiplex even if only the first 8bp of the i7 index are sequenced. The dual index plates are designed such that the index sequence would be unique even if only the first 8bp of i7 were sequenced. However, since you will be demultiplexing using only single index, you will loose the benefit of dual indexing in removing potential index hopped reads.
You will need to enter the first 8 bases of the sample index in the samplesheet to run mkfastq/bcl2fastq.