All Your Base: a fast and accurate probabilistic approach to base calling

Table 1 Summary of data sets analysed and reference genomes used for mapping.

Name	Reference genome	Num. reads	Read length	Paired-end	Date sequenced
ϕX174 L2	ϕX174	677538	76	no	Aug. 2008
ϕX174 L4	ϕX174	1299052	76	no	Aug. 2008
ϕX174 L6	ϕX174	900291	76	no	Aug. 2008
Ibis Test	ϕX174	200000	51	no	Apr. 2009
B. pert.†	B. pertussis Tohama I	4250058	76	yes	Dec. 2009
BGI†	H. sapiens GRCh37	9611783	45	yes	Jul. 2008
Illumina†	H. sapiens GRCh37	13974025	51	yes	Jun. 2008
HiSeq	H. sapiens GRCh37 + ϕX174	7813098	101	yes	Oct. 2010

The individual ends from paired-end sets are referred to with a suffix indicating the end, for example BGI/1, BGI/2. †These sets contain a whole lane; other sets have either been decimated (Ibis Test & HiSeq) or contain only a few tiles (ϕX174 L2, ϕX174 L4 and ϕX174 L6). 'Date sequenced' is approximate, representing our best effort to quantify the vintage of the data. All intensity data are freely available from the AYB website [15] in the Illumina CIF format.

ISSN: 1474-760X