sgdemux

demultiplex

fastq

Description

Demultiplex sequence data generated on Singular Genomics' sequencing instruments.

Input

Name	Type & Properties	Description
--fastqs -f	file required multiple	Path to the input FASTQs, or path prefix if not a file
--sample_metadata -s	file required	Path to the sample metadata CSV file including sample names and barcode sequences

Name

Type & Properties

--fastqs

-f

file

required

multiple

--sample_metadata

-s

file

required

Output

Name	Type & Properties	Description
--sample_fastq	file required output	The directory containing demultiplexed sample FASTQ files.
--metrics	file output	Demultiplexing summary statisitcs: - control_reads_omitted: The number of reads that were omitted for being control reads. - failing_reads_omitted: The number of reads that were omitted for having failed QC. - total_templates: The total number of template reads that were output.
--most_frequent_unmatched	file output	It contains the (approximate) counts of the most prevelant observed barcode sequences that did not match to one of the expected barcodes. Can only be created when 'most_unmatched_to_output' is not set to 0.
--sample_barcode_hop_metrics	file output	File containing the frequently observed barcodes that are unexpected combinations of expected barcodes in a dual-indexed run.
--per_project_metrics	file output	Aggregates the metrics by project (aggregates the metrics across samples with the same project) and has the same columns as `--metrics`. In this case, sample_ID will contain the project name (or None if no project is given). THe barcode will contain all Ns. The undetermined sample will not be aggregated with any other sample.
--per_sample_metrics	file output	Tab-separated file containing statistics per sample.

Name

Type & Properties

--sample_fastq

file

required

output

--metrics

file

output

--most_frequent_unmatched

file

output

--sample_barcode_hop_metrics

file

output

--per_project_metrics

file

output

--per_sample_metrics

file

output

Arguments

Name	Type & Properties	Description
--read_structures -r	string multiple	Read structures, one per input FASTQ. Do not provide when using a path prefix for FASTQs
--allowed_mismatches -m	integer	Number of allowed mismatches between the observed barcode and the expected barcode
--min_delta -d	integer	The minimum allowed difference between an observed barcode and the second closest expected barcode
--free_ns -F	integer	Number of N's to allow in a barcode without counting against the allowed_mismatches
--max_no_calls -N	integer	Max no-calls (N's) in a barcode before it is considered unmatchable. A barcode with total N's greater than 'max_no_call' will be considered unmatchable.
--quality_mask_threshold -M	integer multiple	Mask template bases with quality scores less than specified value(s). Sample barcode/index and UMI bases are never masked. If provided either a single value, or one value per FASTQ must be provided.
--filter_control_reads -C	boolean_true	Filter out control reads
--filter_failing_quality -Q	boolean_true	Filter reads failing quality filter
--output_types -T	string multiple	The types of output FASTQs to write. For each read structure, all segment types listed will be output to a FASTQ file. These may be any of the following: - `T` - Template bases - `B` - Sample barcode bases - `M` - Molecular barcode bases - `S` - Skip bases
--undetermined_sample_name -u	string	The sample name for undetermined reads (reads that do not match an expected barcode)
--most_unmatched_to_output -U	integer	Output the most frequent "unmatched" barcodes up to this number. If set to 0 unmatched barcodes will not be collected, improving overall performance.
--override_matcher	string	If the sample barcodes are > 12 bp long, a cached hamming distance matcher is used. If the barcodes are less than or equal to 12 bp long, all possible matches are precomputed. This option allows for overriding that heuristic.
--skip_read_name_check	boolean_true	If this is true, then all the read names across FASTQs will not be enforced to be the same. This may be useful when the read names are known to be the same and performance matters. Regardless, the first read name in each FASTQ will always be checked.
--sample_barcode_in_fastq_header	boolean_true	If this is true, then the sample barcode is expected to be in the FASTQ read header. For dual indexed data, the barcodes must be `+` (plus) delimited. Additionally, if true, then neither index FASTQ files nor sample barcode segments in the read structure may be specified.
--metric_prefix	string	Prepend this prefix to all output metric file names
--lane -l	integer multiple	Select a subset of lanes to demultiplex. Will cause only samples and input FASTQs with the given `Lane`(s) to be demultiplexed. Samples without a lane will be ignored, and FASTQs without lane information will be ignored

Name

Type & Properties

--read_structures

-r

string

multiple

--allowed_mismatches

-m

integer

--min_delta

-d

integer

--free_ns

-F

integer

--max_no_calls

-N

integer

--quality_mask_threshold

-M

integer

multiple

--filter_control_reads

-C

boolean_true

--filter_failing_quality

-Q

boolean_true

--output_types

-T

string

multiple

--undetermined_sample_name

-u

string

--most_unmatched_to_output

-U

integer

--override_matcher

string

--skip_read_name_check

boolean_true

--sample_barcode_in_fastq_header

boolean_true

--metric_prefix

string

--lane

-l

integer

multiple

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
sample_fastq: "$id.$key.sample_fastq.output"  
metrics: "$id.$key.metrics.tsv"  
most_frequent_unmatched: "$id.$key.most_frequent_unmatched.tsv"  
sample_barcode_hop_metrics: "$id.$key.sample_barcode_hop_metrics.tsv"  
per_project_metrics: "$id.$key.per_project_metrics.tsv"  
per_sample_metrics: "$id.$key.per_sample_metrics.tsv"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/sgdemux/main.nf \  
  -params-file params.yaml

sgdemux

Input

Output

Arguments

Run this component

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