Scripts-Descriptions.md

@@ -6,11 +6,10 @@ The scripts used in the processing of the supporting genomic and transcriptomic
 Table of Contents
 * [Gathering Data](#gathering-data)
 * [Assembly Filtering](#assembly-filtering)
-* [TSA Prep](#preparing-tsa-files)
 * [Softmasking Genome](#softmasking-genome)
 * [Genome Statistical Assessment](#genome-statistical-assessment)
 * [Preparing TSA Files](#preparing-tsa-files)
-* [Short Read Alignment](#short-read-alignment)
+* [Evidence Alignment](#evidence-alignment)
 
 
 #### Gathering Data
@@ -46,7 +45,7 @@ Name | Step | Purpose | Input | Expected Output | Notes
 wholegenomebusco.sh | assembly stats | Use [BUSCO](https://busco.ezlab.org/) to assess genome completeness | Length-filtered/softmasked genome assembly & appropriate single-copy ortholog dataset | Genome completeness benchmark results including predicted genes, alignment results & statistics | 
 quast.sh | assembly stats | Uses QUAST to assess quality of genome assemblies | Genome before filtering/softmasking & Genome after filtering/softmasking | Assembly statistics for both inputs |  
 
-#### Preparing TSA
+#### Preparing TSA Files
 Processing the TSA files from NCBI to be used as evidence for genome annotation tool was accomplished by frame-selecting using [TransDecoder](https://github.com/TransDecoder/TransDecoder/wiki) and clustering with [USearch (v9.0)](https://www.drive5.com/usearch/manual9/).    
 
 Name | Step | Purpose | Input | Expected Output | Notes
@@ -56,6 +55,7 @@ usearch.sh | TSA Prep | Uses [USearch v9.0](https://www.drive5.com/usearch/manua
 
 #### Evidence Alignment
 Short-read and TSA evidence were aligned to genome assemblies using [HISAT2](https://ccb.jhu.edu/software/hisat2/manual.shtml) and [GMAP](http://research-pub.gene.com/gmap/src/README), respectively. Before alignment, short-reads evidence was trimmed QC'd using sickle and [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). 
+
 Name | Step | Purpose | Input | Expected Output | Notes
 ---- | ---- | ------- | ----- | --------------- | -----
 fastqc.sh | short-read QC | Uses FastQC to assess read quality | fastq files from short-read libraries | statistics on read quality in HTML |