Updated to include important file

README.md

@@ -107,6 +107,8 @@ spriggan_results
 │   ├── amrfinder_predictions.tsv
 │   ├── amrfinder_summary.tsv
 │   └── selected_ar_genes.tsv
+├── assembly
+│   └── assembly_stats_results.tsv
 ├── bbduk
 │   ├── *.fastq.gz
 │   ├── *.adapter.stats.txt
@@ -122,6 +124,8 @@ spriggan_results
 │   ├── *.html
 │   ├── *.zip
 │   └── fastqc_summary.tsv
+├── gc
+│   └── gc_stats_results.tsv
 ├── kraken
 │   ├── *.kraken2.txt
 │   ├── kraken_results.tsv
@@ -170,12 +174,12 @@ spriggan_results
           └── spades.fasta
 ```
 Notable output files:  
-**spriggan_report.csv** - Summary table of each step in Spriggan  
-**spriggan_multiqc_report.html** - HTML report generated by MultiQC  
-**\*.contigs.fa** - Shovill assembly for each sample  
-**\*.amr.tsv** - AMR genes identified in each sample by AMRFinderPlus  
-**\*.mlst.tsv** - MLST scheme identified for each sample
-**Empty_samples.csv** - Lists any samples that are empty and were removed from the pipeline
+**spriggan_report.csv** - Summary table of each step in Spriggan.
+**spriggan_multiqc_report.html** - HTML report generated by MultiQC.
+**\*.contigs.fa** - Shovill assembly for each sample.
+**\*.amr.tsv** - AMR genes identified in each sample by AMRFinderPlus.
+**\*.mlst.tsv** - MLST scheme identified for each sample.
+**Empty_samples.csv** - Lists any samples that do not have any reads and were removed from the pipeline.
 
 ## Credits
 Spriggan was written by Dr. [Kelsey Florek](https://github.com/k-florek), Dr. [Abigail C. Shockey](https://github.com/AbigailShockey), and [Eva Gunawan](https://github.com/evagunawan).