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 theSampleProject
andSampleID
for lanes 1 and 8, and write the updated sample sheet to the fileSampleSheet2.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 toSampleSheet3.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:
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.