CLC Bio, the Denmark based bioinformatics company, published their annual survey on NGS market. The 2012 NGS survey had about 700 respondents from around the world and it revealed interesting use/application of Next-Gen Sequencing technology and analysis.
Illumina the most preferred NGS Technology
Expectedly, Illumina came on top on the Next-Gen sequencing technology that people work with. Illumina is followed by Roche and Life Tech coming in third. 34.6% of the users work on Illumina HiSeq, 21% of the users work with Illumina MiSeq, and about 21% users are working with Roche GS FLX. On the benchtop sequencers, Illumina MiSeq topped Ion Torrent PGM, with 11.5% users using PGM compared MiSeq’s 21%.
On the applications side, whole genome sequencing, RNA-Seq, and De-Novo sequencing came out on top with 40.8%, 40.1%, and 39.8% of responders using them. The use of whole genome sequencing on top of the application suggests a certain biases of the users participated in the survey.
UCSC and Ensembl are the Most Preferred NGS Tools
UCSC and Ensembl tools topped the preferred open source NGS tools highlighting the value of genomes and their annotations. It is interesting that the large-scale genome resources topped the tools list.
Interestingly, a similar percentage of users had no preferred NGS tool highlighting the diverse state of NGS analysis. Bowtie was the fourth in the list of most preferred tools, followed by Galaxy and Samtools.
Most interestingly, BLAT the good old alignment tool came at the seventh position with 21% of the users liking it. RNA-Seq analysis and BEDtools for further dissecting the alignments were missing in the top NGS tools. The absence of RNA-Seq analysis tools in the preferred NGS tools, despite RNA-Seq being at the top of application list, is interesting/puzzling.
Another interesting outcome of the survey is that about 24% of the responders don’t have access to bioinformaticians.