diff --git a/README.md b/README.md index 7876ec9..ac7b075 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,13 @@ bam-readcount ============= +[![DOI](https://joss.theoj.org/papers/10.21105/joss.03722/status.svg)](https://doi.org/10.21105/joss.03722) +![latest release](https://img.shields.io/github/v/release/genome/bam-readcount) ![tests](https://github.com/seqfu/bam-readcount/actions/workflows/tests.yml/badge.svg?branch=samtools-1.10) ![coverage](https://coveralls.io/repos/seqfu/bam-readcount/badge.svg?branch=samtools-1.10&service=github) +![Docker Pulls](https://img.shields.io/docker/pulls/mgibio/bam-readcount?style=plastic) +![GitHub](https://img.shields.io/github/license/genome/bam-readcount) + `bam-readcount` is a utility that runs on a `BAM` or `CRAM` file and generates low-level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, @@ -13,6 +18,10 @@ Originally designed to help filter genomic mutation calls, the metrics `bam-read are also useful as input for variant detection tools and for resolving ambiguity between variant callers. +If you find `bam-readcount` useful in your work, please cite our [paper](https://doi.org/10.21105/joss.03722): + +> Khanna et al., (2022). Bam-readcount - rapid generation of basepair-resolution sequence metrics. _Journal of Open Source Software_, 7(69), 3722. https://doi.org/10.21105/joss.03722 + Contents --------- * [Installation](#installation)