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Handling sequencing run data

Illumina sequencing runs

The reference_prep_sample_sheet utility can be used for editing and clean-up of sample sheet files that are used as input to the Fastq generation process, including converting between different sample sheet formats.

Examples:

  1. Read in the sample sheet file SampleSheet.csv, update the SampleProject and SampleID for lanes 1 and 8, and write the updated sample sheet to the file SampleSheet2.csv:

    prep_sample_sheet.py -o SampleSheet2.csv --set-project=1,8:Control \
     --set-id=1:PhiX_10pM --set-id=8:PhiX_12pM SampleSheet.csv

  2. Automatically fix spaces and duplicated sampleID/sampleProject combinations and write out to SampleSheet3.csv:

    prep_sample_sheet.py --fix-spaces --fix-duplicates \
     -o SampleSheet3.csv SampleSheet.csv

The bcftbx library also provides classes and functions for handling Illumina sequencing data:

  • ../bcftbx/IlluminaData

See ../background/illumina for details of the data structures of raw and processed Illumina sequencing runs.

SOLiD sequencing runs

The reference_analyse_solid_run utility can be used to report on the primary data from a run of a SOLiD sequencer instrument, and perform various checks and operations those data.

The bcftbx library also provides classes and functions for handling SOLiD sequencing data:

  • ../bcftbx/SolidData
  • ../bcftbx/Experiment

See ../background/solid for details of the directory structure and contents of a SOLiD sequencing run.