Long Ranger1.3, printed on 12/26/2024
The longranger run pipeline is intended for human, germline variant calling and phasing. The longranger basic and longranger align pipelines perform basic barcode processing and alignment to support users developing other Linked-Reads applications.
The longranger basic pipeline performs basic read and barcode processing including read trimming, barcode error correction, barcode whitelisting, and attaching barcodes to reads. It outputs barcode-attached reads either as FASTQ or unaligned BAM. For more details, see the BASIC Pipeline Map.
To run longranger basic, you will need to specify the following parameters:
| Argument | Description |
|---|---|
--id | A unique run ID string: e.g. sample345 |
--fastqs | Path of the FASTQ folder generated by longranger demux e.g. /home/jdoe/runs/HAWT7ADXX/outs/fastq_path |
--bam | (optional) Output as unaligned BAM instead of FASTQ. |
--indices | (optional) Sample indices associated with this sample. Comma-separated list of:
|
--lanes | (optional) Lanes associated with this sample |
After determining these input arguments, run longranger basic:
$ cd /home/jdoe/runs $ longranger basic --id=sample345 \ --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \ --indices=SI-001 \
The output of the pipeline will be contained in a folder named with the sample ID you specified (e.g. sample345). The subfolder named outs will contain the main pipeline output files:
| File Name | Description |
|---|---|
summary.csv | Run summary metrics in CSV format |
barcoded.fastq.gz | Reads with barcodes embedded as a comment of the form: BX:Z:ACTCGACTGACTAG-1 (only generated when --bam is not specified) |
barcoded_aligned.bam | Unaligned BAM containing reads with barcodes attached in the BX tag (only generated when --bam specified) |
The longranger align pipeline performs all of the functions of the longranger basic pipeline, plus aligns the reads with BWA and infers original input molecule extents. For more details, see the ALIGN Pipeline Map.
To run longranger align, you will need to specify the following parameters:
| Argument | Description |
|---|---|
--id | A unique run ID string: e.g. sample345 |
--fastqs | Path of the FASTQ folder generated by longranger demux e.g. /home/jdoe/runs/HAWT7ADXX/outs/fastq_path |
--reference | Path to a 10x compatible reference, e.g. /opt/refdata-hg19-1.2.0.See Installation for how to download and install the default reference. |
--indices | (optional) Sample indices associated with this sample. Comma-separated list of:
|
--lanes | (optional) Lanes associated with this sample |
After determining these input arguments, run longranger align:
$ cd /home/jdoe/runs $ longranger align --id=sample345 \ --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \ --reference=/opt/refdata-hg19-1.2.0 \ --indices=SI-001 \
The output of the pipeline will be contained in a folder named with the sample ID you specified (e.g. sample345). The subfolder named outs will contain the main pipeline output files:
| File Name | Description |
|---|---|
summary.csv | Run summary metrics in CSV format |
possorted_bam.bam | Aligned reads annotated with barcode information |
possorted_bam_index.bam.bai | Index for possorted_bam.bam |