MiSeq Index Filtering

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Facts & Details: 

In a joint project with Dr Jun Wang and Prof. John Baines of the Max Planck Institute for Evolutionary Biology, we have been working on reducing the Illumina MiSeq Platform errors. One of the strategies we employed was to quality filter the index sequences (MIDs). By default the MiSeq instrument allows one mismatch on the index sequences, regardless of whether one or two index sequences were used. We found that mismatches in the indices, as well as low quality indices increase the rate of erroneous sequences in the benchmarking of 16S rRNA sequencing, and we thus provide a script enabling filtering of index sequences (submitted):


The data we used for the manuscript can be found here:
filter_miseq_index.pl

V1-V2 region sequenced on 454 Roche platform (de-multiplexed, index filtered):
454_V1V2_fastq.zip

V4 region sequenced on Miseq platform (de-multiplexed, index filtered):
Miseq_V4_fastq.zip

V1-V2 region sequenced on Miseq platform, index reads are re-derived from base-calls:
Miseq_V1V2_fastq.zip


Dr Jun Wan can now be contacted at: jun [dot] wang [at] med [dot] kuleuven [dot] be