modules/popscle_freemuxlet

Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available.

popscledemultiplexinggenotype-based deconvoltionsingle cell

https://github.com/nf-core/modules/[...]/modules/nf-core/popscle/freemuxlet

Description

Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available.

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1']

`plp:directory`

Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup.

`n_sample:integer`

Number of samples multiplexed together.

Output

name:type

description

pattern

`result`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`*.clust1.samples.gz:file`

Output file contains the best guess of the sample identity, with detailed statistics to reach to the best guess.

*.clust1.samples.gz

`vcf`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`*.clust1.vcf.gz:file`

Output vcf file for each sample inferred and clustered from freemuxlet.

*.clust1.vcf.gz

`lmix`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`*.lmix:file`

Output file contains basic statistics for each barcode.

*.lmix

`singlet_result`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`*.clust0.samples.gz:file`

Optional output file contains the best sample identity assuming all droplets are singlets when writing auxiliary output files is turned on.

*.clust0.samples.gz

`singlet_vcf`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`*.clust0.vcf.gz:file`

Optional output vcf file for each sample inferred and clustered from freemuxlet assuming all droplets are singlets when writing auxiliary output files is turned on.

*.clust0.vcf.gz

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

popscle
Apache-2.0

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools

github.com/statgen/popscle 10.1038/nbt.4042