Visit to Poland: Roche 454 GS Junior Data

I was visiting my friend Miroslaw Kwasniewski an Assistant Professor at the University of Silesia in Katowice, Poland. He is got a GS Junior 454 machine which I wanted to check out. Besides that, he wanted some help with their bioinformatics servers and pipelines.

I was just looking at one dataset, transcriptomics from barley, obtained from the GS Junior, and read counts, read lengths and quality are all great, very impressive. I have some statistics obtained using FastQC, after exporting the SFF file from GS Junior to FastQ format using sff_extract.

This is the distribution of the read quality on a per base basis. As you can see, reads can be well over 400, around 500bp with Phred qualities above 20.

The sequence length distribution has a nice peak around 500 bp.

GS Junior could achieve 100.000 reads throughput, Mirek was getting 150.000 reads.

GS Junior seem to be quite good for sequencing low complexity samples. Quality and length of the sequencing reads is great, but depth for a e.g., full transcriptome in angiosperms, would be either challenging or too expensive. It is great for amplicon sequencing, bacterial genome sequencing, virus genome sequencing, i.e., would be great for the phages (!).