Description

Demultiplex bgzip’d fastq files

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

sample_sheet:file

sample_sheet file (either a Singular Genomics sample sheet, or a two column csv wih Sample_Barcode and Sample_ID)

*.{csv}

fastqs_dir:directory

Input directory containing bgzipped (not gzip) FASTQ files

Output

name:type
description
pattern

sample_fastq

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

output/*_R*.fastq.gz:file

Demultiplexed per-sample FASTQ files

output/*_R*.fastq.gz

metrics

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

output/metrics.tsv:file

Demultiplexing summary stats; control_reads_omitted failing_reads_omitted, total_templates

output/metrics.tsv

most_frequent_unmatched

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

output/most_frequent_unmatched.tsv:file

File containing approx. counts of barcodes that did not match the expected barcodes

output/most_frequence_unmatched.tsv

per_project_metrics

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

output/per_project_metrics.tsv:file

Summary metrics for samples in the same project

output/per_project_metrics.tsv

per_sample_metrics

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

output/per_sample_metrics.tsv:file

Summary metrics for each sample

output/per_sample_metrics.tsv

sample_barcode_hop_metrics

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

output/sample_barcode_hop_metrics.tsv:file

File output for dual-indexed runs with barcodes which are unexpected combinations of expected barcodes e.g. expected barcodes = AA-TT/GG-CC and observed barcodes = AA-CC/GG-TT

output/sample_barcode_hop_metrics/tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

sgdemux
For Singular G4™ Sequencing Platform only

Tool for demultiplexing sequencing data generated on Singular Genomics' sequencing instruments.