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10x Genomics
Chromium Genome & Exome

Long Ranger BASIC and ALIGN Pipelines

The longranger wgs and longranger targeted pipelines are 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.

Long Ranger BASIC

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:

ArgumentDescription
--idA unique run ID string: e.g. sample345
--fastqsPath of the FASTQ folder generated by longranger mkfastq
e.g. /home/jdoe/runs/HAWT7ADXX/outs/fastq_path
--sample(optional) Sample name as specified in the sample sheet supplied to mkfastq.
--bam(optional) Output as unaligned BAM instead of FASTQ.

After determining these input arguments, run longranger basic:

$ cd /home/jdoe/runs
$ longranger basic --id=sample345 \
                   --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path

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 NameDescription
summary.csvRun summary metrics in CSV format
barcoded.fastq.gzReads with barcodes embedded as a comment of the form: BX:Z:ACTCGACTGACTAGCT-1 (only generated when --bam is not specified)
barcoded_aligned.bamUnaligned BAM containing reads with barcodes attached in the BX tag (only generated when --bam specified)

Long Ranger ALIGN

The longranger align pipeline performs all of the functions of the longranger basic pipeline, plus aligns the reads with the Lariat aligner 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:

ArgumentDescription
--idA unique run ID string: e.g. sample345
--fastqsPath of the FASTQ folder generated by longranger mkfastq
e.g. /home/jdoe/runs/HAWT7ADXX/outs/fastq_path
--sample(optional) Sample name as specified in the sample sheet supplied to mkfastq.
--referencePath to a 10x compatible reference, e.g. /opt/refdata-hg19-2.1.0.
See Installation for how to download and install the default reference.

After determining these input arguments, run longranger align:

$ cd /home/jdoe/runs
$ longranger align --id=sample345 \
                   --reference=/opt/refdata-hg19-2.1.0 \
                   --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path

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 NameDescription
summary.csvRun summary metrics in CSV format
possorted_bam.bamAligned reads annotated with barcode information
possorted_bam.bam.baiIndex for possorted_bam.bam