MiSeq

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The Illumina MiSeq

Illumina MiSeq runs produces paired-end data with read lengths of 150 bp, 250 bp or 300 bp. The run time for a standard 2x150bp run is 24 hours with the 300 bp reads taking just under two days. Typically there is only a short queue to use this instrument with 250 bp runs processed within 10 working days (including how QC steps for each pool). Other run types may take longer to process depending on how quickly we can get the reagents from Illumina. The output is supplied as standard gzip compressed Fastq files.

NextSeq(s) vs MiSeq data comparison

Machine Data generation
NextSeq 2K The NextSeq 2K sequences about 400 or 1,100 million read pairs per lane for 100, 200 or 300 cycle runs. Each lane can be run as a single or paired end lane with the total length of the reads equaling the number of cycles in the kit. The read lenghts do not have to be equal, but long reads sigificantly other 150 bp are not recommended.
NextSeq The NextSeq 500 sequences either 130 or 400 million inserts per lane with 75, 150 or 300 cycle kits.
MiSeq Typically sequences over than 10 or 20 million inserts depending on the sequencing chemistry per lane from a 2x150 bp, 2x250 bp or 2x300 bp sequencing run.