Long Ranger2.1, printed on 11/23/2024
Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants. There are five main pipelines, each triggered by a longranger command:
longranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files.
longranger wgs takes demultiplexed FASTQ files from a whole genome sample and performs alignment, de-duplication and filtering, and uses the Chromium molecular barcodes to call and phase SNPs, indels, and structural variants.
longranger targeted takes demultiplexed FASTQ files from a targeted sample, such as an exome, and performs alignment, de-duplication and filtering, and uses the Chromium molecular barcodes to call and phase SNPs, indels, and structural variants. Reads are aligned to the whole genome, but statistics are reported only on the pulled-down regions in the supplied target BED file.
longranger basic takes FASTQ files from longranger mkfastq and performs basic barcode processing including error correction, barcode white-listing, and attaching barcodes to reads.
longranger align performs the steps in the basic pipeline plus aligns reads and infers input molecules.
These pipelines combine Chromium-specific algorithms with widely used components such as BWA, Freebayes, and GATK. Output is delivered in standard BAM, VCF, and BEDPE formats that are augmented with long range information.
Long Ranger supports the following Chromium sequencing workflows:
Whole Genome
Performs alignment and calling and phasing of SNPs, indels, and structural variants. Requires, as input, sequencing data from a 40X Chromium whole genome run. This corresponds to 128Gb of raw sequence for a human genome.
Targeted
Performs alignment and calling and phasing of SNPs, indels, and structural variants. Targeting the whole exome requires, as input, sequencing data from a 60-80X Chromium exome run. This corresponds to 9Gb of raw sequence for the Agilent V6 Exome.