Replace generic README with specific one

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>

README.md

@@ -1,94 +1,52 @@
-<p align="center">
+# NanoSim
-  <img src="singularity-builds-artwork.svg" alt="Logo" width="400">
-</p>
 
-# Singularity Builds
+[![Container source](https://img.shields.io/static/v1?label=Container%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/MillironX/singularity-builds/tree/nanosim)
+[![NanoSim source](https://img.shields.io/static/v1?label=NanoSim%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/bcgsc/NanoSim)
+[![Version 3.0.2](https://img.shields.io/static/v1?label=Latest%20version&message=1.99.2&color=yellowgreen&logo=linuxcontainers&style=flat-square)](https://cloud.sylabs.io/library/millironx/default/nanosim)
+[![Docs](https://img.shields.io/static/v1?label=Docs&message=README&color=blue&style=flat-square)](https://github.com/bcgsc/NanoSim/blob/master/README.md)
+[![Alpine base](https://img.shields.io/static/v1?label=Base%20image&message=Alpine&color=0d597f&logo=alpinelinux&style=flat-square)](https://www.alpinelinux.org/)
 
-[![Sylabs Cloud Library](https://img.shields.io/static/v1?label=Sylabs%20Cloud%20Library&message=millironx/default&color=yellowgreen&logo=linuxcontainers&style=flat-square)](https://cloud.sylabs.io/library/millironx/default)
+NanoSim is a fast and scalable read simulator that captures the
-[![MIT License](https://img.shields.io/github/license/MillironX/singularity-builds?style=flat-square)](https://github.com/MillironX/singularity-builds/blob/master/LICENSE.md)
+technology-specific features of ONT data, and allows for adjustments upon
+improvement of nanopore sequencing technology.
 
-Definition files for building [Nextflow]-compatible [Singularity] container
+## Tools installed
-images to use in bioinformatics pipelines. Programs get containers in this
-repository if I can't find an up-to-date container that also has Nextflow's
-dependencies installed (usually `bash` and `ps` are the culprits). All of these
-images are available on the [Sylabs Cloud Library] for easy access.
 
-## Get started
+### Minimap2
 
-1. [Install Singularity]
+- `minimap2`
-2. Enter the container, e.g.
 
-    ```bash
+### LAST
-    singularity shell library://millironx/default/julia:latest
-    ```
 
-3. Execute commands, e.g.
+- `lastdb`
+- `lastal`
+- `last-split`
+- `last-merge-batches`
+- `last-pair-probs`
+- `lastdb8`
+- `lastal8`
+- `last-split8`
+- `fastq-interleave`
+- `last-dotplot`
+- `last-map-probs`
+- `last-postmark`
+- `last-train`
+- `maf-convert`
+- `maf-join`
+- `maf-sort`
+- `maf-swap`
+- `parallel-fasta`
+- `parallel-fastq`
 
-    ```shellsession
+### Samtools
-    Singularity> julia
-                   _
-       _       _ _(_)_     |  Documentation: https://docs.julialang.org
-      (_)     | (_) (_)    |
-       _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
-      | | | | | | |/ _` |  |
-      | | |_| | | | (_| |  |  Version 1.6.1 (2021-04-23)
-     _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
-    |__/                   |
 
-    julia>
+- `samtools`
-    ```
 
-## Where else to find container images
+### GenomeTools
 
-### State Public Health Bioinformatics (StaPH-B) Dockerfiles
+- `gt`
 
-[:globe_with_meridians: Website](https://staph-b.github.io/) -
+### NanoSim
-[:octocat: GitHub](https://github.com/StaPH-B/docker-builds) -
-[:whale: Docker hub](https://hub.docker.com/u/staphb)
 
-All of these images are tested for Nextflow and Singularity compatability, and
+- `read_analysis.py`
-are updated on a regular basis. I've even contributed to their repository.
+- `simulator.py`
-
-### Niema Moshiri's Dockerfiles
-
-[:octocat: GitHub](https://github.com/Niema-Docker) -
-[:whale: Docker hub](https://hub.docker.com/u/niemasd)
-
-Slim bioinformatics images based on Alpine Linux with useful (but optional)
-common combinations.
-
-### Biocontainers Registry
-
-[:globe_with_meridians: Website](https://biocontainers.pro/) -
-[:octocat: GitHub](https://github.com/BioContainers/containers) -
-[:whale: Docker hub](https://hub.docker.com/u/biocontainers)
-
-Most of these images are already in Singularity format, and there are _a lot_ of
-tools for the picking here.
-
-### McDonnell Genome Institute
-
-[:octocat: GitHub](https://github.com/orgs/genome/repositories?language=dockerfile) -
-[:whale: Docker hub](https://hub.docker.com/u/mgibio)
-
-These folks make high-quality and well-maintained images for their own and
-other tools.
-
-## Artwork
-
-Artwork was designed by [@MillironX] by remixing:
-
-- [DNA] by Scout (Public domain)
-- [Cardboard box] by Rushtini (Public domain)
-- [Pointing Boy in Baseball Cap] by ruthirsty (Public domain)
-- [Singularity Logo] by Sylabs (BSD 3-Clause)
-
-[Nextflow]: https://nextflow.io
-[Singularity]: https://sylabs.io/singularity
-[Sylabs Cloud Library]: https://cloud.sylabs.io/library/millironx/default
-[Install Singularity]: https://sylabs.io/guides/3.8/admin-guide/installation.html
-[@MillironX]: https://github.com/MillironX
-[DNA]: https://openclipart.org/detail/192915/dna
-[Cardboard box]: https://openclipart.org/detail/192915/dna
-[Pointing Boy in Baseball Cap]: https://openclipart.org/detail/281363/pointing-boy-in-baseball-cap
-[Singularity Logo]: https://github.com/sylabs/singularity/blob/master/docs/logos/singularity_v3.svg