Quick start changes

src/quickstart.md

@@ -14,3 +14,32 @@ For x64 Linux, run:
 curl --proto '=https' --tlsv1.2 -LsSf "https://github.com/DavidsonGroup/nailpolish/releases/download/nightly_develop/nailpolish" -o nailpolish
 chmod +x nailpolish
 ```
+
+### Get test files
+
+Download the `scmixology2` subset reads using:
+
+```shell
+wget https://github.com/DavidsonGroup/nailpolish/releases/download/sample-fastq-for-quickstart/scmixology2_sample.fastq
+```
+
+## Indexation
+
+By default, nailpolish expects the barcode and UMI to be in the `@BC_UMI` format at the start of the header.
+Alternative barcode and UMI formats can be provided through either a preset (one of `bc-umi`, `umi-tools`, `illumina`)
+or a custom barcode regex.
+
+```shell
+# write the index file to `index.tsv`
+nailpolish index --index index.tsv scmixology2_sample.fastq
+```
+
+## Summary of duplicate count
+
+A .html file can be generated to summarise some key statistics about the input reads.
+
+```shell
+nailpolish summary index.tsv
+```
+
+![nailpolish summary](./assets/summary_image.png)