fastq_demultiplexer

Converts fastq single cell data from MGI (10x converted library) to Illumina compatible format.

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Installation

go install github.com/overerd/fastq_demultiplexer@latest

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Arguments

Required:

• -1|--r1 and -2|--r2 expect an R1-R2 pair of fastq files.
• -c|--csv-file table with barcodes for each index.
• -o|--output-directory output directory (would contain subdirectories of demultiplexed samples).

Optional:

• -s|--csv-separator barcode csv-file separator (default: ',').
• --targets-file path to file with targets (if null, would select all possible indexes from barcodes file).
• --transform-strategy strategy of how to transform fastq data (supported strategies: 10x, 10x_no_index) (default: 10x)
• --filename-template filename template (default: '{{.SampleName}}_S{{.SampleNumber}}L00{{.LaneNumber}}{{.ReadType}}_001.fastq.gz').
• --lane-number lane number for selected fastq pair (default: 1).
• --buffer-size sets buffer size in bytes for reading fastq files (should be set and increased if necessary to avoid "take too long" error when reading fastq files with long lines) (default: 10 * 1024 * 1024).
• --block-size sets buffer size for accumulating multiple paired reads in transformation pipeline (default: 4 * 2 * 1024).
• --compression-level output gzip compression level if applicable [1, 9] (default: 1).
• --debug enables debug messages.

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Filename template:

It uses golang template syntax {{.Variable}}.

Template {{.SampleName}}_S{{.SampleNumber}}_L00{{.LaneNumber}}_{{.ReadType}}_001.fastq.gz would result in filenames like H2_S1_L001_R2_001.fastq.gz.

Supported template variables:

• {{.SampleName}} - index name from barcodes csv-file
• {{.SampleNumber}} - index number
• {{.LaneNumber}} - --lane-number value
• {{.ReadType}} - read type (could be R1, R2 and I1)

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Example

fastq_demultiplexer \
    -1 v350013347_run65_L01_read_1.fq.gz \
    -2 v350013347_run65_L01_read_2.fq.gz \
    -c Single_Index_Kit_T_Set_A.csv \
    --lane-number 1 \
    --block-size 1000 \
    --targets-file targets.txt \
    --transform-strategy 10x_no_index \
    --filename-template {{.SampleName}}_S{{.SampleNumber}}_L00{{.LaneNumber}}_{{.ReadType}}_001.fastq.gz \
    -o output/ \
    --debug