README.Rmd

---
title: "README"
author: "S Namba"
date: "`r Sys.Date()`"
output:
  md_document: 
    variant: markdown_github
---

# simlady

SIMulator for Long read transcriptome Analysis with RNA DecaY model

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, comment = "")
```


## Installation

```{bash install, eval=FALSE}
git clone https://github.com/shinichinamba/simlady.git
cd simlady
pip3 install .
```


## Usage

```{bash help_code, eval=FALSE}
simlady --help
```

```{bash help, echo=FALSE}
export PATH=$HOME/.local/bin:$PATH
simlady --help
```


## Error model

Simlady uses the Pacific Biosciences SMRT error model which is implemented in [SimLoRD](https://bitbucket.org/genomeinformatics/simlord/src/master/).


## Citation

S Namba *et al*. Multi-sample Full-length Transcriptome Analysis of 22 Breast Cancer Clinical Specimens with Long-Read Sequencing. ***BioRxiv*** (2020) https://doi.org/10.1101/2020.07.15.199851