Updating readme

README.md

@@ -1,12 +1,33 @@
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 ![snakemaker](https://github.com/AnimalGenomicsETH/bovine-assembly/workflows/snakemaker/badge.svg?branch=master)
 
-# bovine-assembly
+# Bovine pangenomes
 
-Currently under active development. This repo contains pipelines designed to assembly, validate, and compare bovine assemblies for multiple sequencing technologies and assembler strategies.
 
-## Purpose
-Can assemble given data into genomes and then validate quality
+## Genome assembly
+
+This repository contains pipelines and scripts used to assemble, validate, and compare bovine genomes using ONT and HiFi data for three trios
+  - Original Braunvieh x Original Braunvieh
+  - Nellore x Brown Swiss
+  - gaur x Piedmontese
+
+For multiple current long read assemblers assemblers like hifiasm, canu, Shasta, Flye, etc.
+
+
+## Pangenome analysis
+
+There are also multiple pipelines and scripts used to construct different pangenomes with minigraph and subsequent analysis of the SVs like repeatitive content and accuracy scores.
+
+## Citation
+
+Details on the results can be found in our [manuscript](https://www.biorxiv.org/content/10.1101/2021.11.02.466900v2), or the assemblies hosted [here](https://doi.org/10.5281/ZENODO.5906579). 
+
+> **Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies**
+> 
+> Alexander S. Leonard, Danang Crysnanto, Zih-Hua Fang, Michael P Heaton, Brian L. Vander Ley, Carolina Herrera, Heinrich Bollwein, Derek M. Bickhart, Kristen L. Kuhn, Timothy PL. Smith, Benjamin D. Rosen, Hubert Pausch
+> 
+> bioRxiv 2021.11.02.466900; doi: https://doi.org/10.1101/2021.11.02.466900
+
 
 ## Usage
-modify parameters in `snakepit/run_parameters.yaml` and run as `snakemake`. More details and linking to the [LSF](https://github.com/AnimalGenomicsETH/snakemake_lsf) profile coming soon.
+Many of the parameters are tuned to run for our data and on the ETH Euler cluster, using for example a forked version of the LSF snakemake [profile](https://github.com/AnimalGenomicsETH/snakemake_lsf), so it may take some modifying to work smoothly in different contexts. Many tools are assumed to be available in $PATH, but all are freely available.