BCL files

Posted Posted in bioinformatics, sequencing

As part of the Primary Analysis Illumina sequencing machines measure the intensity of the channels used for encoding the different bases and identify the most likely base at a given position of a sequencing read (tag). The Real Time Analysis (RTA) software writes the base and the confidence in the call as a quality score to base call (.bcl) files. As the name implies this is done in real time, i.e. for every cycle of the sequencing run a call for every location identified on the flow cell (tiles and lanes) is added. Bcl files are stored in binary format and represent the raw data output of a sequencing run. The format is described here. Software such as Casava/BclToFastq, Eland or the iSAAC aligner can make use of these files.

The *.bcl files are stored in the BaseCalls directory:

<run directory>/Data/Intensities/BaseCalls/L<lane>/C<cycle>.1

They are named in the format:


If you want to overcome errors during downstream processing from missing calls, software such as iSAAC and configureBclToFastq have an “–ignore-missing-bcl” command line option. This will interpret missing *.bcl files as no call (N) at that position.

Sources: Illumina, SeqAnswers

Embryo Morphology Assessment

Posted Posted in IVF, technology

Some researchers and clinicians believe embryo morphology and development characteristics can be used to assess the viability of IVF embryos to increase chances of a successful pregnancy.

Healthy embryos, i.e. the most viable zygotes that will develop into blastocysts and further seem to follow a specific growth pattern between development day 3 and re-implantation on day 5:
Growth from 2 to 3 cells should be seen in 9 – 11 hours, from 3 to 4 cells in under 2 hours. Reaching day 5 is a critical as the embryo will be re-implanted into the uterus and will attach to the endometrium. The normal development process is shown in figure 1 (source: CMFT NHS):

Embryo Morphology Assessment

Embryo morphology is graded on a scale of 1 to 5 as shown in fig 2 (source: CMFT NHS):

Embryo Morphology Assessment

Embryo cell division can be monitored through the use of an “embryoscope”, an incubator with integrated camera. Time-lapse pictures are analysed by an embryologist to help select viable embryos. Systems that help the monitoring process are e.g. the “Early Embryo Viability Assessment” (Eeva) software by Auxogyn.

Embryo Morphology Assessment

Cell tracking and embryo assessment with Eeva (YouTube)

Further readings: