genomicslab/lrtools repository overview

⁠LRtools

LRtools is a long read analysis package developed by Wang Genomics Lab. It contains three tools:

1- LongReadSum⁠ : a QC analysis tool for generating statistical summary and plots for sequencing data

2- NanoCaller⁠: a deep-learning based haplotype-aware variant caller for detecting SNPs and small indels from error-prone long reads

3- LIQA⁠ (Long-read Isoform Quantification and Analysis): an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data

Use the following commands to run each tool:

⁠LongReadSum

docker run genomicslab/lrtools:<tag> LongReadSum

⁠NanoCaller

docker run genomicslab/lrtools:<tag> NanoCaller --help
docker run genomicslab/lrtools:<tag> NanoCaller_WGS --help

⁠LIQA

docker run genomicslab/lrtools:<tag> liqa