biopet / 10xkit

TenxKit

Tools - CellReads

This tool will generate a histogram of reads per cell barcode. This can be used to validate output from cellranger or to set a alternative cutoff.

Tools - CellVariantcaller

This tool will call variants based on 10x data. Usually the output of cellranger is used. Each cell will be treated a separated sample.

Tools - CalulateDistance

This tool will calculate for each cell combination a sum of distances. The distances are the relative distance to the middle line for each allele divided by the total coverage on that position.

Tools - GroupDistance

This tool we try to group distances together. The result should be a clusters of 1 single sample.

This tool will execute multiple iterations to find the groups.

Tools - MergeBams

This tool can merge separated 10x experiments into a single bam file. This is used to simulate a mixed run. This is used as a control for the GroupDistance tool.

Tools - EvalSubGroups

This tool will compare all given groups. The histogram for a Correct match should be a steep histogram starting at 0. When multiple peaks are seen this might be a mixture of samples.

Tools - ExtractGroupVariants

This tool will merge variants from the same group. This will be a representation of the real samples. This can also be used to validate if there is a true set known.

Tools - ExtractCellFastqs

This tools will extract fastq files for a given list of cell barcodes. All reads that are marked as duplicate or secondary will be skipped by default.

Documentation

For documentation and manuals visit our github.io page.

About

TenxKit is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of a pipeline, for example the SASC team's biowdl pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.

Contact

For any question related to TenxKit, please use the github issue tracker or contact the SASC team directly at: [email protected].