All sequencing data will be available for secure download via our SLIMS server.
Illumina sequencing data will be delivered as compressed FASTQ files. By default the data will be de-multiplexed (e.g. split according to sample). Each SLIMS directory will further contain a file with the de-multiplexing metrics and a file listing md5 checksums for all the FASTQ files. The checksums can be used to verify that the data integrity has been preserved your download/data transfer.
You will receive all the full-length reads passing the Illumina quality filter. Please contact us if you would like to receive the data quality-trimmed, adapter-trimmed, or adapter-filtered.
For PacBio sequencing you will receive all the data generated by the PacBio SMRT-Portal pipeline (raw data and primary analysis data) including FASTA and FASTQ files as well as the “bax.h5” and “.xml” files required to re-run the analyses. By default we are running also subread filtering as the secondary analysis (except for large gnome projects where this is not required) or other appropriate secondary analysis pipelines for bacterial genome assembly, amplicon analysis, or Iso-seq analyses. You will receive the complete secondary analysis data sets.