README.md

Samplesheet_converter

v1.1

Written by Chuan Wang (chuan-wang@github), 2017-03-08

These scripts are for the purpose of converting Illumina samplesheet that contains Chromium 10X indexes for demultiplexing.

Headers and lines with ordinary indexes will be passed without any change. Lines with Chromium 10X indexes will be expanded into 4 lines, with 1 index in each line, and suffix 'Sx' will be added at the end of sample names.

Example:

Script:

python main.py -i <inputfile> -o <outputfile> -x <indexlibrary>

Original samplesheet:

[Header]
Investigator Name,Chuan Wang
Date,None
Experiment Name,Project_001
[Reads]
151
151
[Data]
Lane,SampleID,SampleName,SamplePlate,SampleWell,index,index2,Project,Description
1,Sample_101,101,HGWT5ALXX,1:1,SI-GA-A1,,Project_001,
1,Sample_102,102,HGWT5ALXX,1:1,SI-GA-B1,,Project_001,
2,Sample_103,103,HGWT5ALXX,2:1,SI-GA-C1,,Project_001,

Modified samplesheet:

[Header]
Investigator Name,Chuan Wang
Date,None
Experiment Name,Project_001
[Reads]
151
151
[Data]
Lane,SampleID,SampleName,SamplePlate,SampleWell,index,index2,Project,Description
1,Sample_101_S1,101_S1,HGWT5ALXX,1:1,GGTTTACT,,Project_001,
1,Sample_101_S2,101_S2,HGWT5ALXX,1:1,CTAAACGG,,Project_001,
1,Sample_101_S3,101_S3,HGWT5ALXX,1:1,TCGGCGTC,,Project_001,
1,Sample_101_S4,101_S4,HGWT5ALXX,1:1,AACCGTAA,,Project_001,
1,Sample_102_S1,102_S1,HGWT5ALXX,1:1,GTAATCTT,,Project_001,
1,Sample_102_S2,102_S2,HGWT5ALXX,1:1,TCCGGAAG,,Project_001,
1,Sample_102_S3,102_S3,HGWT5ALXX,1:1,AGTTCGGC,,Project_001,
1,Sample_102_S4,102_S4,HGWT5ALXX,1:1,CAGCATCA,,Project_001,
2,Sample_103_S1,103_S1,HGWT5ALXX,2:1,CCACTTAT,,Project_001,
2,Sample_103_S2,103_S2,HGWT5ALXX,2:1,AACTGGCG,,Project_001,
2,Sample_103_S3,103_S3,HGWT5ALXX,2:1,TTGGCATA,,Project_001,
2,Sample_103_S4,103_S4,HGWT5ALXX,2:1,GGTAACGC,,Project_001,