Merge pull request #159 from alermol/readme_update

Update README.md

Author: joshfactorial

README.md

@@ -109,48 +109,35 @@ template config file to copy and use for your runs.
 
 To run the simulator in parallel with the same config file and significantly speed up runtime, please see the [Parallelization](#parallelization) section.
 
-reference: full path to a fasta file to generate reads from
-read_len: The length of the reads for the fastq (if using). Integer value, default 101.
-coverage: desired coverage value. Float or int, default = 10
-ploidy: Desired value for ploidy (# of copies of each chromosome in the organism). Default is 2
-paired_ended: If paired-ended reads are desired, set this to True. Setting this to true requires
-    either entering values for fragment_mean and fragment_st_dev or entering the path to a
-    valid fragment_model.
-fragment_mean: Use with paired-ended reads, set a fragment length mean manually
-fragment_st_dev: use with paired-ended reads, set the standard deviation of the fragment length dataset
+`reference`: full path to a fasta file to generate reads from    
+`read_len`: The length of the reads for the fastq (if using). _Integer value, default 101._    
+`coverage`: desired coverage value. _Float or int, default = 10_    
+`ploidy`: Desired value for ploidy (# of copies of each chromosome in the organism). _Default is 2_    
+`paired_ended`: If paired-ended reads are desired, set this to True. Setting this to true requires either entering values for fragment_mean and fragment_st_dev or entering the path to a valid fragment_model.    
+`fragment_mean`: Use with paired-ended reads, set a fragment length mean manually    
+`fragment_st_dev`: Use with paired-ended reads, set the standard deviation of the fragment length dataset
 
 The following values can be set to true or omitted to use defaults. If True, NEAT will produce the file type.
 The default is given:
 
-produce_bam: False
-produce_vcf: False
-produce_fastq: True
-
-error_model: full path to an error model generated by NEAT. Leave empty to use default model
-    (default model based on human, sequenced by Illumina)
-mutation_model: full path to a mutation model generated by NEAT. Leave empty to use a default
-    model (default model based on human data sequenced by Illumina)
-fragment_model: full path to fragment length model generate by NEAT. Leave empty to use default model
-    (default model based on human data sequenced by Illumina)
-
-threads: The number of threads for NEAT to use.
-    Note: this feature is not yet fully implemented
-avg_seq_error: average sequencing error rate for the sequencing machine. Use to increase or
-    decrease the rate of errors in the reads. Float betwoon 0 and 0.3. Default is set by the error model.
-rescale_qualities: rescale the quality scores to reflect the avg_seq_error rate above. Set True to activate if you 
-    notice issues with the sequencing error rates in your datatset.
-include_vcf: full path to list of variants in vcf format to include in the simulation. These will be inserted as they 
-    appear in the input VCF into the final VCF, and the corresponding fastq and bam files, if requested.
-target_bed: full path to list of regions in bed format to target. 
-    All areas outside these regions will have coverage of 0.
-discard_bed: full path to a list of regions to discard, in BED format.
-mutation_rate: Desired rate of mutation for the dataset. Float between 0.0 and 0.3
-    (default is determined by the mutation model)
-mutation_bed: full path to a list of regions with a column describing the mutation rate of that region,
-    as a float with values between 0 and 0.3. The mutation rate must be in the third column as, e.g., mut_rate=0.00.
-rng_seed: Manually enter a seed for the random number generator. Used for repeating runs. Must be an integer.
-min_mutations: Set the minimum number of mutations that NEAT should add, per contig. Default is 0. We recommend setting 
-    this to at least one for small chromosomes, so NEAT will produce at least one mutation per contig. |
+`produce_bam`: False    
+`produce_vcf`: False    
+`produce_fastq`: True    
+
+`error_model`: full path to an error model generated by NEAT. Leave empty to use default model _(default model based on human, sequenced by Illumina)_     
+`mutation_model`: full path to a mutation model generated by NEAT. Leave empty to use a default model _(default model based on human data sequenced by Illumina)_     
+`fragment_model`: full path to fragment length model generate by NEAT. Leave empty to use default model _(default model based on human data sequenced by Illumina)_
+
+`threads`: The number of threads for NEAT to use. _Note: this feature is not yet fully implemented_
+`avg_seq_error`: average sequencing error rate for the sequencing machine. Use to increase or decrease the rate of errors in the reads. _Float between 0 and 0.3. Default is set by the error model._    
+`rescale_qualities`: rescale the quality scores to reflect the avg_seq_error rate above. Set True to activate if you  notice issues with the sequencing error rates in your datatset.    
+`include_vcf`: full path to list of variants in vcf format to include in the simulation. These will be inserted as they appear in the input VCF into the final VCF, and the corresponding fastq and bam files, if requested.    
+`target_bed`: full path to list of regions in bed format to target. All areas outside these regions will have coverage of 0.    
+`discard_bed`: full path to a list of regions to discard, in BED format.    
+`mutation_rate`: Desired rate of mutation for the dataset. _Float between 0.0 and 0.3 (default is determined by the mutation model)_    
+`mutation_bed`: full path to a list of regions with a column describing the mutation rate of that region, as a float with values between 0 and 0.3. The mutation rate must be in the third column as, e.g., mut_rate=0.00.    
+`rng_seed`: Manually enter a seed for the random number generator. Used for repeating runs. _Must be an integer._    
+`min_mutations`: Set the minimum number of mutations that NEAT should add, per contig. _Default is 0._ We recommend setting this to at least one for small chromosomes, so NEAT will produce at least one mutation per contig.
 
 The command line options for NEAT are as follows: