Monthly Archives: February 2014

New Illumina platforms and software support

It has been a while since I blogged last time. Life has been really busy after my relocation and still trying to adjust to Atlanta. But here is my latest post: I just attended an Illumina platform demonstration seminar and found a few interesting things.

1) 2X150 bp PE reads from NextSeq 500 has roughly 75% or more reads above Q30, which is similar to the MiSeq and HiSeq platforms introduced years back.

2) NextSeq 500 uses fast 2-channel SBS technology for base detection. So instead of using 4 colors (as in MiSeq and HiSeq), it uses only red or green for base color detection. Unlike MiSeq there is no analysis software installed on the machine. Analysis software is external (and supported by BaseCloud platform, maybe others too).

3) NextSeq uses a base-calling software similar to current MiSeq software.

4) The MiSeq software was written from scratch using C# and will replace the historical CASAVA software written mainly in C.

It is interesting that the C#-based code will replace CASAVA for future Illumina platforms and HiSeq does not use the fast 2-channel SBS technology.

Other interesting things:

5) Illumina recommends to use BWA and GACT for variant calling, although this decision was based on the prefernce of the external user community and Illumina is aware that GACT was designed for diploid chromosomes.

6) Illumina has no answer about mixed read sequence interpretation.