LRTK

Linked-Read ToolKit (LRTK), is a unified and versatile toolkit to process human and metagenomic linked-read sequencing data from different linked-read sequencing technologies, including 10x Genomics, single-tube long fragment read (stLFR) and transposase enzyme linked long-read sequencing (TELL-Seq). LRTK provides functions to simulate linked-read sequencing data, perform barcode correction, barcode-aware alignment and metagenome assembly, reconstruction of virtual DNA fragments, and barcode-assisted genomic variant detection and phasing. LRTK also has the ability to perform automatic analysis from raw sequencing data to downstream analysis and support the analysis of multiple samples in parallel. In addition, LRTK could produce publication-ready visualizations and generate reproducible reports, summarizing the key parameters at multiple checkpoints such as library preparation.