Updates formatting of README

README.md

@@ -18,10 +18,10 @@ Analyse the proportion of genic read bases aligned by GraphAligner.
 ```python analyse_gaf_genic.py gaffile blastfile reads.fa outfile.txt```
 
 Input/Output:
- - gaffile: graphical alignment file produced by [Graphaligner](https://github.com/maickrau/GraphAligner)
- - blastfile: [BLAST](https://www.sciencedirect.com/science/article/abs/pii/S0022283605803602?via%3Dihub) output file in tabular format generated from exact alignment of gene sequences from [Lees et al.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930550/) (aligned files are '*_dna.fa') to simulated genomes (```blastn -outfmt 6 -perc_identity 100 -qcov_hsp_perc 100```)
- - reads.fa: read sequences used in alignment in FASTA format, generated by [Nanosim-H](https://github.com/karel-brinda/NanoSim-H)
- - outfile.txt: output summary file
+ - ```gaffile```: graphical alignment file produced by [Graphaligner](https://github.com/maickrau/GraphAligner)
+ - ```blastfile```: [BLAST](https://www.sciencedirect.com/science/article/abs/pii/S0022283605803602?via%3Dihub) output file in tabular format generated from exact alignment of gene sequences from [Lees et al.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930550/) (aligned files are '*_dna.fa') to simulated genomes (```blastn -outfmt 6 -perc_identity 100 -qcov_hsp_perc 100```)
+ - ```reads.fa```: read sequences used in alignment in FASTA format, generated by [Nanosim-H](https://github.com/karel-brinda/NanoSim-H)
+ - ```outfile.txt```: output summary file
 
  ### analyse_gaf_total.py
 
@@ -30,8 +30,8 @@ Analyse the proportion of total read bases aligned by GraphAligner.
 ```python analyse_gaf_total.py gaffile outfile.txt```
 
 Input/Output
-- gaffile: graphical alignment file produced by [Graphaligner](https://github.com/maickrau/GraphAligner)
-- outfile.txt: output summary file
+- ```gaffile```: graphical alignment file produced by [Graphaligner](https://github.com/maickrau/GraphAligner)
+- ```outfile.txt```: output summary file
 
 ### analyse_nodes.py
 
@@ -40,8 +40,8 @@ Analyse node length and degree from a GFA file.
 ```python analyse_nodes.py gfafile outpref```
 
 Input/Output
-- gfafile: GFA file produced produced from graph construction
-- outpref: output prefix for distribution and summary files
+- ```gfafile```: GFA file produced produced from graph construction
+- ```outpref```: output prefix for distribution and summary files
 
 ### analyse_unitig.py
 
@@ -50,9 +50,9 @@ Analyse unitig frequencies from a Bifrost graph.
 ```python analyse_unitig.py gfa_dist.txt colours.tsv output```
 
 Input/Output
-- gfa_dist.txt: Distribution file generated from analyse_nodes.py
-- colours.tsv: TSV file produced from [Bifrost](https://github.com/pmelsted/bifrost) query by querying constituent unitigs against GFA itself
-- output: output file of results
+- ```gfa_dist.txt```: Distribution file generated from analyse_nodes.py
+- ```colours.tsv```: TSV file produced from [Bifrost](https://github.com/pmelsted/bifrost) query by querying constituent unitigs against GFA itself
+- ```output```: output file of results
 
 ### bifrost_unitig_freq.R
 
@@ -70,10 +70,10 @@ Checks presence of a called ORF in forward and reverse complements of a set of r
 ```check_ORF_in_ref(ref_fasta_for, ref_fasta_rev, query_fasta, outfasta)```
 
 Input/Output
-- ref_fasta_for: Multi-FASTA of reference source sequences (forward strand)
-- ref_fasta_rev: Multi-FASTA of reference source sequences (reverse strand)
-- query_fasta: ORF calls in FASTA format
-- outfasta: output FASTA containing ORFs not present in forward or reverse sequences.
+- ```ref_fasta_for```: Multi-FASTA of reference source sequences (forward strand)
+- ```ref_fasta_rev```: Multi-FASTA of reference source sequences (reverse strand)
+- ```query_fasta```: ORF calls in FASTA format
+- ```outfasta```: output FASTA containing ORFs not present in forward or reverse sequences.
 
 #### check_ref_in_query()
 
@@ -83,9 +83,9 @@ Checks presence of a known gene in longer called ORFs.
 ```check_ref_in_query(ref_fasta, query_fasta, outfile)```
 
 Input/Output
-- ref_fasta: Multi-FASTA of known genes
-- query_fasta: ORF calls in FASTA format
-- outfile: output FASTA containing known genes not found in any called ORFs
+- ```ref_fasta```: Multi-FASTA of known genes
+- ```query_fasta```: ORF calls in FASTA format
+- ```outfile```: output FASTA containing known genes not found in any called ORFs
 
 ### compare_gene_calls.py
 
@@ -94,10 +94,10 @@ Compares known genes against called ORFs by Prodigal/ggCaller in S. pneumoniae c
 ```python compare_gene_calls.py reference_genes gene_calls caller_type group```
 
 Input/Output
-- reference_genes: known genes in FASTA format
-- gene_calls: ORF calls by [Prodigal](https://github.com/hyattpd/Prodigal) or [ggCaller](https://github.com/samhorsfield96/ggCaller) in FASTA format
-- caller_type: specify which caller used (ggCaller = ggc, Prodigal = prod)
-- group: CBL group used in comparison.
+- ```reference_genes```: known genes in FASTA format
+- ```gene_calls```: ORF calls by [Prodigal](https://github.com/hyattpd/Prodigal) or [ggCaller](https://github.com/samhorsfield96/ggCaller) in FASTA format
+- ```caller_type```: specify which caller used (ggCaller = ggc, Prodigal = prod)
+- ```group```: CBL group used in comparison.
 
 ### gfa_to_fasta.py
 
@@ -107,7 +107,7 @@ Creates FASTA of unitigs from GFA files
 ```gfa_to_fasta(gfafile)```
 
 Input/Output
-- gfafile: GFA file generated from graph construction
+- ```gfafile```: GFA file generated from graph construction
 - output is FASTA with same file prefix as gfafile
 
 ### panaroo_gene_freq.R