For each sequencing run, the Real-Time Analysis (RTA) software of your Illumina machine generates a BCL file with basic base calls and associated quality values (Q scores). This is true for most modern Illumina machines, including NextSeq, NoveSeq and others. However, most NGS analysis software require a FASTQ file as input and cannot work with BCL files.
You can send your data directly to Illumina BaseSpace (to the cloud) and convert your data there
Drawbacks: upload/download time, data security & compliance
Illumina offers the commandline tool bcl2fastq, which can be used for conversion on your local computer. Unfortunately, this solution is only offered for the Linux operating systems and not for Windows
Drawbacks: different operating system, IT expert needed
Both solutions are in no way user-friendly.
We would like to introduce our Windows tool ecBclConvert! Using this tool it is now possible to easily convert BCL files into the FASTQ file format directly on a Windows machine. No upload to the cloud, no IT expert who has to set up and maintain a Linux system needed.
Last updated on November 22, 2019
ecSeq is a bioinformatics solution provider with solid expertise in the analysis of high-throughput sequencing data. We organize public workshops and conduct on-site trainings on NGS data analysis.
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