From 98a8e981264052b18a5c15c9cc10dc198d538732 Mon Sep 17 00:00:00 2001 From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com> Date: Mon, 27 Nov 2023 14:19:10 +0100 Subject: [PATCH] updated readme --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 7ffafbe..412dd01 100755 --- a/README.md +++ b/README.md @@ -1,9 +1,5 @@ VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data =============== -[![Build Status](https://travis-ci.org/cbg-ethz/shorah.svg?branch=master)](https://travis-ci.org/cbg-ethz/viloca) -[![Bioconda package](https://img.shields.io/conda/dn/bioconda/shorah.svg?label=Bioconda)](https://bioconda.github.io/recipes/viloca/README.html) -[![Docker container](https://quay.io/repository/biocontainers/shorah/status)](https://quay.io/repository/biocontainers/viloca) - VILOCA is an open source project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools @@ -23,7 +19,11 @@ pip install git+https://github.com/cbg-ethz/VILOCA@master ``` ### Example -To test your installation, we recommend running the program on `tests/data_1`. +To test your installation run VILOCA `tests/data_1`: +``` +viloca run -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode use_quality_scores +``` + If the sequencing amplicon strategy is known, we recommend using the amplicon-mode of the program, which takes as input the `.insert.bed` - file: `viloca run -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode use_quality_scores`