Handling sequencing run data

Illumina sequencing runs

The prep_sample_sheet.py 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:

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
```
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 Illumina sequencing data for details of the data structures of raw and processed Illumina sequencing runs.

SOLiD sequencing runs

The analyse_solid_run.py 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:

See SOLiD sequencing data for details of the directory structure and contents of a SOLiD sequencing run.