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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

sample_fastq (file)

Demultiplexed per-sample FASTQ files

output/*_R*.fastq.gz

metrics (file)

Demultiplexing summary stats; control_reads_omitted failing_reads_omitted, total_templates

output/metrics.tsv

most_frequent_unmatched (file)

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

output/most_frequence_unmatched.tsv

per_project_metrics (file)

Summary metrics for samples in the same project

output/per_project_metrics.tsv

per_sample_metrics (file)

Summary metrics for each sample

output/per_sample_metrics.tsv

sample_barcode_hop_metrics (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
included in
demultiplex
maintainers
Github user nh13
Github user sam-white04
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

sgdemux
For Singular G4™ Sequencing Platform only

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

github.com/Singular-Genomics/singular-demux github.com/Singular-Genomics/singular-demux#sgdemux