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Guides Instructions for reformat functionality

Introduction

This functionality is performed with the command reformat. It is to reformat reads demultiplexed by splitBarcode tool provided by MGI into illumia format and generates quality reports explained at mgikit reports page.

This command should be used for each sample separately (either paired-end or single-end). if you have multiple samples, you need to process each of them individually.

Command arguments

  • -f or --read1: the path to the forward reads fastq file for both paired-end and single-end input data.

  • -r or --read2: the path to the reverse reads fastq file.

  • -i or --input: the path to the directory that contains the input fastq files.

  • -o or --output: The path the output directory.

    The tool will create the directory if it does not exist or overwrite the content if the directory exists and the parameter --force is used. The tool will exit with an error if the directory exists, and --force is not used. If this parameter is not provided, the tools will create a directory (in the working directory) with a name based on the date and time of the run as follows mgiKit_Y-m-dTHMS. where Y, m, d, H, M, and S are the date and time format.

  • --reports: The path of the output reports directory.

    By default, the tool writes the files of the run reports in the same output directory as the

    demultiplexed fastq files (-o or --output parameter). This parameter is used to write the reports in a different folder as specified with this parameter.

  • --lane: Lane number such as L01.

    This parameter is used to provide the lane number when the parameter -i or --input is not

    provided. The lane number is used for QC reports and it is mandatory when Illumina format is requested for file naming.

  • --instrument: The id of the sequncing machine.

    This parameter is used to provide the instrument id when the parameter -i or --input is not provided. The parameter is mandatory when Illumina format is requested for read header and file naming.

  • --run: The run id. It is taken from Bioinf.csv as the date and time of starting the run.

    This parameter is used to provide the run id when the parameter -i or --input is not provided. The parameter is mandatory when Illumina format is requested for read header and file naming.

  • --writing-buffer-size: The default value is 67108864. The size of the buffer for each sample to be filled with data then written once to the disk. Smaller buffers will need less memory but makes the tool slower. Largeer buffers need more memory.

  • --compression-level: The level of compression (between 0 and 12). 0 is fast but no compression, 12 is slow but high compression. [default: 1]

  • --force: this flag is to force the run and overwrite the existing output directory if exists.

  • --flexible: By default, the tool will calculate the length of the first read and its all parts and use this information in the analysis for a quicker determination of the read boundaries. --flexible option, will make the tool determine the read boundaries based on the new line character (\n).

  • --info-file: The name of the info file that contains the run information. Only needed when using the --input parameter. [default: BioInfo.csv]

  • --disable-illumina: reads will be left as is and only quality reports will be generated.

  • --umi-length: The length of UMI expected at the end of the read (r1 for single-end, or r2 for paired-end) [Default: 0].

  • --report-level: The level of reporting. 0 no reports will be generated, 1 data quality and demultiplexing reports. 2: all reports (reports on data quality, demultiplexing, undetermined and ambiguous barcodes).[default: 2]

  • --sample-index: The index of the sample in the sample sheet. It is required for file naming. [default: 1]

  • --barcode: The barcode of the specific sample to calculate the mismatches for the reports. If not provided, no mismatches will be calculated.

Usage Examples

1. Demultiplexing a run with dual indexes (i7 and i5)

target/release/mgikit  reformat \
    -f testing_data/input/extras_test/FC01_L01_sample1_1.fq.gz \
    -r testing_data/input/extras_test/FC01_L01_sample1_2.fq.gz \
    --lane L01 -o output \
    --sample-index 1 \
    --info-file testing_data/input/extras_test/BioInfo.csv
Contributors
Ziad Al-Bkhetan