Next generation sequencing
CF Genomics operates a set of Illumina benchtop sequencers – 2x NextSeq 500, 2x MiSeq. These machines cover broad range of possible applications including whole-genome sequencing, exome sequencing, RNA-Seq, ChIP-Seq and other counting applications, metagenomics (16S, 18S) and many others. These instruments have single lane flowcells and ready-to-use cartridges with sequencing chemistry.
NextSeq supports up to 300 cycles sequencing (ie. 2x150), flow cells are available in two sizes – Mid Output with expected output 100-150M reads (150 or 300 sequencing cycles) and High Output with expected output 300-500M reads (75, 150 and 300 cycles). Compared to HiSeq 2500, NextSeq Mid Output corresponds to ½ of HiSeq v4 lane and High Output to 1 ½ HiSeq v4 lane, compared to HiSeq 3000/4000 Mid Output is approx. 1/3 of lane and High Output corresponds to 1 HiSeq lane. NextSeq is good choice for many applications ranging from larger gene panels and exomes through counting applications such as RNA-Seq or ChIP-Seq to whole transcriptome or genome sequencing.
MiSeq supports longer reads (up to 2x300bp), capacity is 1-25 millions reads/run. For standard size flowcells expected number of reads is 10-20M for v2 chemistry available for 50, 300, and 500 cycles of sequncing (ie. up to 2x250) and 15-25M for v3 chemistry that is available in 150 or 600 cycles variants. Smaller flow cells are available for 300 and 500 sequencing cycles but its price/output ratio is suboptimal. MiSeq is best in applications that do not require high number of reads and/or require long reads for example 16S , gene panels, small genomes.