Long Ranger2.0, printed on 12/22/2024
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 four main pipelines, each triggered by a longranger command:
longranger demux wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files.
longranger run takes demultiplexed FASTQ files and performs alignment, de-duplication and filtering, and uses the Chromium molecular barcodes to call and phase SNPs, indels, and structural variants.
longranger basic takes FASTQ files from longranger demux 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 (128Gb) whole genome run.
Exome
Performs alignment and calling and phasing of SNPs, indels, and structural variants. Requires, as input, BCL sequencing data from an 60-80X Chromium (9Gb) exome run.