Long Ranger1.3, printed on 04/28/2024
Long Ranger is a set of analysis pipelines that processes GemCode 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 GemCode-prepared sequencing samples and to convert barcode and read data to FASTQ files.
longranger run takes FASTQ files from longranger demux and performs alignment, de-duplication and filtering, and uses the GemCode 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 GemCode-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 GemCode sequencing workflows:
Whole Genome
Performs alignment and calling and phasing of SNPs, indels, and structural variants. Requires, as input, BCL sequencing data from a 60X GemCode whole genome run, or a 23X GemCode run plus an existing VCF file.
Exome
Performs alignment and calling and phasing of SNPs, indels, and structural variants. Requires, as input, BCL sequencing data from a 160X GemCode exome run.