WES of Mus musculus on vehicle: 229 Thy
Genome Quebec uses an open-source pipeline for the basic analysis of Illumina runs. The pipeline runs the Illumina demultiplexer (bcl2fastq2) and the alignment is with STAR for anything that is RNA; with bwa_mem for the rest, including libraries of unknown types (which can be RNA). The aligner used (and its version) can be found in the @PG header of the bam file (samtools view -H name_of_the_bam_file.bam; look at the line starting with @PG, usually the last one). Genome Quebec does the alignment only for QC: they don't clip the adapters and don't trim the reads.