--libraries_file
     A tab-delimited text file that provides output name, R1 fastq file,
     marker info file, and optionally: R2 fastq file, marker name, filter
     seq file. See sample template (make sure new line characters can be 
     parsed by Perl in a UNIX environment).

     --options_file      
     A tab-delimited text file. First column is "reads", "families", 
     or "variants" to indicate the which script the option applies to.
     The second column is the option. See sample template.

     --reads_script      
     Full path to MDS_process_reads.pl if not in working directory

     --families_script      
     Full path to MDS_process_families.pl if not in working directory

     --variants_script      
     Full path to MDS_process_variants.pl if not in working directory

     perl MDS_process_pipeline.pl \
     	--libraries_file=INPUT_FILE --options_file=OPTIONS_FILE \
       	--reads_script=/PATH/TO/SCRIPTS/MDS_process_reads.pl \
       	--families_script=/PATH/TO/SCRIPTS/MDS_process_families.pl \
       	--variants_script=/PATH/TO/SCRIPTS/MDS_process_variants.pl

     --r1_fastq
     File containing Illumina read 1 MDS sequences (raw sequences). Can 
     be gzipped.

     --marker_info_file
     A tab-delimited text file that reports marker names, primers, and 
     reference sequences

     --r2_fastq
     File containing Illumina read 2 MDS sequences (raw sequences) if
     paired-end sequencing was performed. If provided, bbmerge.sh will
     be run to collapse fwd and rev reads. Can be gzipped.

     --marker_name [default: first name in Marker Information File]
     Name of MDS marker found within Marker Information File

     --output [default: r1_fastq file name]
     Base name for all output files (additional extensions will be added)

     --bbmerge_exe [default: bbmerge.sh]      
     Full path to bbmerge.sh if not in default PATH

     --bbmerge_trimq [default: 20]   
     Quality score used for trimq parameter in bbmerge.sh

     --bbmerge_minoverlap [default: 30]   
     Sequence length for minoverlap parameter in bbmerge.sh

     --bbmerge_mismatches [default: 5]   
     Maximum number of mismathces for mismatches parameter in bbmerge.sh

     --disable_cutadapt 
     Add this flag to turn off primer trimming with cutadapt.

     --cutadapt_exe [default: cutadapt]      
     Full path to cutadapt if not in default PATH

     --cutadapt_err_tol [default: 0.15]   
     Error tolerance for cutadapt trimming

     --cutadapt_cores [default: 4]   
     Number of cores to request for cutadapt step. This may need to be set
     to 1 if using a cutadapt version with Pyhton v2.

     --cutadapt_min_len [default: 1]   
     Value for minimum_length parameter in cutadapt

     --cutadapt_report_untrimmed   
     Add this flag to export a fastq file with reads that are not primer-
     trimmed by cutadapt (regardless, these reads are not used in
     subsequent analysis steps).

     --barcode_len [default: 14] 
     Number of Ns in the random barcode (unique molecular identifier) at
     beginning of each MDS reads.

	--disable_rep_filter
	Add this flag to turn off the default filter that excludes reads with
	MDS barcodes that are just one long homopolymer (e.g. AAAAAAAAAAAAAA).

	--min_optical_dist [default: 0]
	Minimum pixel distance for retaining a read with the same barcode as 
	another read on the same tile within the same Illumina flow cell.
	Specifying non-zero values here will help eliminate optical/clustering
	duplicates (MDS ideally only compares amplification duplicates).

	--min_tile_edge_dist [default: 0]
	Minimum pixel distance for X and Y coordinates on the Illumina tile.
	Specifying a non-zero value will help eliminate tile-edge duplicates
	(MDS ideally only compares amplification duplicates). Note that this 
	option will discard lots of non-duplicate reads. It just discards all
	reads within that distance of left/bottom tile edge.

	--min_barcode_qual [default: 20]
	Discard reads that have basecalls in barcode with quality value lower
	than this.

	--phred_offset [default: 33]
	ASCII offset value for quality score encoding. 33 is standard for
	current Illumina runs.

	--disable_n_filter
	Add this flag to turn off the default filter that excludes reads with
	MDS barcodes that contain an N.

	--delete_intermediate_fastqs
	Add this flag to delete the large intermediate fastq files and only
	the final merged/trimmed file.

     perl MDS_process_reads.pl \
     	--r1_fastq=READ1.fastq.gz -r2_fastq=READ2.fastq.gz \
     	--marker_info_file=MDS_markers.txt --marker_name=At_mt1 \
     	--min_optical_dist=5000 --min_tile_edge_dist=2000 \
     	--delete_intermediate_fastqs \
     	--output=my_output

     --input
     Trimmed fastq output from MDS_process_reads.pl

     --output [default: fastq input name]
     Base name for all output files (additional extensions will be added)

     --min_len_agreement [default: 0.8]   
     Minimum proportion of reads with the same length within a read family.
     Families below this level will be excluded from further analysis.

	--suppress_var_len_output
	Add this flag to avoid outputing fasta file summarizing read families
	with variation in read length.

	--min_base_qual [default = 20]
	Change any basecalls with a quality score below this to N. These bases
	will be excluded from summary calculations.

	--exclude_n_reads
	Add this flag to remove the entire read if it contains any Ns.

	--phred_offset [default: 33]
	ASCII offset value for quality score encoding. 33 is standard for
	current Illumina runs.

     perl MDS_process_families.pl \
     	--exclude_n_reads \
     	--input=Trimmed_Input.fq --output=my_output

     --input
     Read fams output text file from MDS_process_families.pl

     --marker_info_file
     A tab-delimited text file that reports marker names, primers, and 
     reference sequences

     --output [default: input file name]
     Base name for all output files (additional extensions will be added)

     --marker_name [default: first name in Marker Information File]
     Name of MDS marker found within Marker Information File

     --min_base_agreement [default: 0.8]   
     Minimum proportion of reads with the same basecall within a read family.
     Bases below this level will be excluded from further analysis.

     --min_len_fasta [default: 3]
     Read families with consensus length different from reference will be
     output to fasta file if they have a family size larger than this value.   

     --min_snp_fasta [default: 3]
     Read families with SNP variant calls will be output to fasta file if 
     they have a family size larger than this value.   

     --min_multisnp_fasta [default: 2]
     Read families with more than one SNP variant (but with the expected reference
     length) will be output to a fasta file if they have at least this many 
     SNPs. This file should be checked for non-specific amplicons that happen
     to be the correct length (can greatly inflate variant call rates).
     Note that this option does not affect the tabulation of counts in the "single"
     output files. These treat any sequence with >1 SNPs as multivariant.

	--suppress_fasta_output
	Add this flag to avoid outputing fasta files summarizing with variants seqs.

	--exclude_n_families
	Add this flag to exclude the entire sequence from any read families that have
	an N at any position in their consensus sequences.

	--filter_seq_file
	Simple text file with one sequence per line (no headers or other content).
	Read families with consensus sequences that are exact, full-length matches to any
	of the sequences in this file will be excluded from statistical analysis. This 
	can be used to filter known contaminants like NUMTs.

     perl MDS_process_variants.pl \
     	--marker_info_file=MDS_markers.txt --marker_name=At_mt1 \
     	--min_base_agreement=1 \
     	--input=INPUT_READ_FAMS_FILE.txt --output=my_output

     --input_lib_list
     Inputs can be provided with in a simple text file (one library per line) with
     this option.
     
     Or they can be provided as a space-delimited list at the end of the command
     line call.   

Family Size Threshold for Variant Frequencies

     --fam_size_freqs
     A cutoff for read family size. All families of this size and larger will be 
     pooled for reporting variant frequencies.
    
Family Size Threshold for Variant Sprectrum and Position-Specific Information

     --fam_size_spect
     A cutoff for read family size. All families below this size will be discarded
     for variant-spectrum and position-distribution summaries.

     --output [default: input file name]
     Base name for all output files (additional extensions will be added)

     --include_multisnps
     Add this flag to include read families that have multiple variants relative to 
     the reference. By default, only families with a single SNP are used. If this 
     option is specified, mutliSNP families should have been manually inspected to
     confirm that they are genuine.

     perl MDS_aggregate_variants.pl \
     	--input_lib_list=INPUT_LIB_LIST_FILE \
     	--fam_size_freqs=5 --fam_size_spect=5 \
     	--output=my_output 

     perl MDS_aggregate_variants.pl \
     	--fam_size_freqs=5 --fam_size_spect=5 \
     	--output=my_output \
     	Lib1 Lib2 Lib3 ...