Supporting evidence for applicability of QQ-SNV for SNV calling on Illumina NGS sequencing data of any read length. (PDF 32 kb

Bie Verbist (758342)

Herman van Vlijmen (3537107)

Jeroen Aerssens (584848)

Joke Reumers (5867)

Kim Thys (446679)

Koen Van der Borght (3537110)

Lieven Clement (203038)

Yves Wetzels (3537104)

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Additional file 5: of QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

Supplementary Tables. Sequence and error profile of HIV plasmids (Tables S1-S3). Training performance of QQ-SNV (Table S4), performance of QQ-SNV on in silico HIV plasmid mixture ground set (Table S5) and performance of QQ-SNV on HIV, HCV and H1N1 test sets (Tables S6-S10). (PDF 84 kb

Additional file 2: of QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

Supporting evidence for stability of coefficients in the QQ-SNV companion logistic regression recalibration model. (PDF 6 kb

Additional file 3: of QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

QQ-SNV. The ZIP archive contains the following three files: the main perl script file to be executed QQ-SNV_workflow.pl and the SAS files QQ-SNV.sas and get_quantiles.sas. To test QQ-SNV, the read alignment files in SAM format for the HCV plasmid mixture data (downsampled 40Â %) and the HCV 1b reference file in FASTA format can be downloaded from http://sourceforge.net/projects/qqsnv. To run QQ-SNV execute the following command: perl QQ-SNV_workflow.pl. (ZIP 5 kb

Additional file 4: of QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

https://figshare.com/articles/Additional_file_2_of_QQ-SNV_single_nucleotide_variant_detection_at_low_frequency_by_comparing_the_quality_quantiles/4425635

Additional file 5: of QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

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