GenomeComb

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Filter Selection

Supplementary Data Reumers, De Rijk et al

Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)

GenomeComb

Select genome comparison and filter setting

We have used GenomeComb to compare within-platform replicates (monozygotic twin genomes, Complete Genomics technology), and cross-platform replicates (Yoruban NA19240 sequenced using Illumina GAII and Complete Genomics). Extensive filter combinations were tested on these genome comparisons, and for each filter combination several metrics are reported:

• Fraction of shared variants
• Fraction of discordant variants
• Fraction of reference genome
• Per variant error rate
• Per base error rate

Usage:

Here you can choose which genomes to compare (i.e twins or NA19240), which which coverage stringency should be used (i.e. relaxed setting or minimal coverage depth of 10 versus stringent setting or minimak coverage depth of 20). After selecting the genomes to compare different filters can be applied manually, or certain predefined settings can be used.

To browse these results, first select which genomes you want to compare:

Complete Genomics Twin Genomes       Low coverage depth cutoff 20 Low coverage depth cutoff 10

Yoruban NA19240 CG/Illumina GAII   Illumina SNV filtering versus the Complete Genomics (CG) genome   Low coverage depth cutoff 20 No filtering on CG Stringent filtering on CG   Low coverage depth cutoff 10 No filtering on CG Stringent filtering on CG   CG SNV filtering versus the Illumina (ILL) genome   Low coverage depth cutoff 20 No filtering on CG Stringent filtering on CG   Low coverage depth cutoff 10 No filtering on CG Stringent filtering on CG